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SeqShop: Sequence Mapping and Assembly Practical, June 2014 (view source)

Revision as of 11:07, 2 February 2017

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→‎Download the example data
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'''Note:''' the latest version of this practical is available at: [[SeqShop: Sequence Mapping and Assembly Practical]]
 +
* The ones here is the original one from the June workshop (updated to be run from elsewhere)
 +
 
== Introduction ==
 
== Introduction ==
−
See the [[introductory slides]] for an intro to this tutorial.
+
See the [[Media:SeqShop - GotCloud Align.pdf|introductory slides]] for an intro to this tutorial.
 +
 
 
== Goals of This Session ==
 
== Goals of This Session ==
 
* What we want to learn  
 
* What we want to learn  
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** How to evaluate the quality of sequence data
 
** How to evaluate the quality of sequence data
 
** How to visualize sequence data to examine the reads aligned to particular genomic positions
 
** How to visualize sequence data to examine the reads aligned to particular genomic positions
 +
 +
== Setup in person at the SeqShop Workshop ==
 +
''This section is specifically for the SeqShop Workshop computers.''
 +
<div class="mw-collapsible mw-collapsed" style="width:600px">
 +
''If you are not running during the SeqShop Workshop, please skip this section.''
 +
<div class="mw-collapsible-content">
       
{{SeqShopLogin}}
 
{{SeqShopLogin}}
   −
== Setup your run environment==
+
=== Setup your run environment===
    
This will setup some environment variables to point you to
 
This will setup some environment variables to point you to
−
* GotCloud program
+
* [[GotCloud]] program
 
* Tutorial input files
 
* Tutorial input files
 
* Setup an output directory
 
* Setup an output directory
 
  source /home/mktrost/seqshop/setup.txt
 
  source /home/mktrost/seqshop/setup.txt
 +
* You won't see any output after running <code>source</code>
 +
** It silently sets up your environment
 
<div class="mw-collapsible mw-collapsed" style="width:200px">
 
<div class="mw-collapsible mw-collapsed" style="width:200px">
 
View setup.txt
 
View setup.txt
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
[[File:setup.png|300px]]
+
[[File:setup.png|500px]]
 +
</div>
 +
</div>
 
</div>
 
</div>
 
</div>
 
</div>
    +
== Setup when running on your own outside of the SeqShop Workshop ==
 +
''This section is specifically for running on your own outside of the SeqShop Workshop.''
 +
<div class="mw-collapsible" style="width:600px">
 +
''If you are running during the SeqShop Workshop, please skip this section.''
 +
<div class="mw-collapsible-content">
 +
=== Download & Build GotCloud ===
 +
If you do not already have GotCloud:
 +
* cd to where you want GotCloud installed (you can change this to any directory you want)
 +
mkdir -p ~/seqshop
 +
cd ~/seqshop/
 +
* download, decompress, and build the version of gotcloud that was tested with this tutorial:
 +
wget https://github.com/statgen/gotcloud/archive/gotcloud.workshop.tar.gz
 +
tar xvf gotcloud.workshop.tar.gz
 +
mv gotcloud-gotcloud.workshop gotcloud
 +
cd gotcloud/src
 +
make
 +
cd ../..
 +
 +
Remember the path to gotcloud/ that is what you will need to set your GC variable to.
 +
 +
=== Download the example data ===
 +
Download and untar file containing the example data used in the practicals:
 +
wget http://csg.sph.umich.edu//mktrost/seqshopExample.tar.gz
 +
tar xvf seqshopExample.tar.gz
 +
 +
You will see the names of all the files included in the example data scrolling on the screen as they are unpacked from the tar file.
   −
Alternatively, if you would like to change the output directory, copy the file, make the modifications and source your own file:
+
{{SeqShopRemoteEnv}}
−
cp /home/mktrost/seqshop/setup.txt ~/setup.txt
  −
nedit ~/setup.txt
  −
source ~/setup.txt
  −
(You can use your favorite editor instead of nedit. I typically use emacs, but nedit is more like Windows.)
     −
== Examining Raw Sequence Reads ==
+
== Examining [[GotCloud]] Align Input Files ==
 +
=== Examining Raw Sequence Reads : FASTQs ===
 
FASTQ : standard file format provided to you by those who did the sequencing.
 
FASTQ : standard file format provided to you by those who did the sequencing.
 
: For more information on the FASTQ format, see: http://en.wikipedia.org/wiki/FASTQ_format
 
: For more information on the FASTQ format, see: http://en.wikipedia.org/wiki/FASTQ_format
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* Subset of FASTQs - should map to chromosome 22 36000000-37000000
 
* Subset of FASTQs - should map to chromosome 22 36000000-37000000
   −
  ls ${IN}/fastq/
+
  ls ${SS}/fastq/
 
There are 24 fastq files: combination of single-end & paired-end.  
 
There are 24 fastq files: combination of single-end & paired-end.  
   Line 58: Line 95:     
Look at a couple of FASTQs:
 
Look at a couple of FASTQs:
−
  less -S ${IN}/fastq/HG00551.SRR190851_1.fastq
+
  less -S ${SS}/fastq/HG00551.SRR190851_1.fastq
 
<code>less</code> is a Linux command that allows you to look at a file.
 
<code>less</code> is a Linux command that allows you to look at a file.
−
*<code>-S</code> option prevents line wrap.
+
*<code>-S</code> option prevents line wrap
−
* Use the arrow (up/down/left/right) keys to scroll through the file.
+
* Use the arrow (up/down/left/right) keys to scroll through the file
−
* Use <code>zless</code> if the file is compressed.
+
* Use the <code>space bar</code> to jump down a page
 
Use <code>'q'</code> to exit out of <code>less</code>
 
Use <code>'q'</code> to exit out of <code>less</code>
 
  q
 
  q
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Look at the paired read:
 
Look at the paired read:
−
  less -S ${IN}/fastq/HG00551.SRR190851_2.fastq  
+
  less -S ${SS}/fastq/HG00551.SRR190851_2.fastq  
 +
 
 +
Remember, use <code>'q'</code> to exit out of <code>less</code>
 +
q
    
;Do you notice something in common?
 
;Do you notice something in common?
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</ul>
 
</ul>
 
</ul>
 
</ul>
−
  −
== GotCloud Alignment Pipeline==
  −
  −
[[File:AlignDiagram.png|500px]]
  −
  −
=== Why GotCloud?===
  −
* Easy to learn & run
  −
** All-in-one sequence analysis pipeline
  −
** You don’t have to know the details of individual component
  −
* Robust parallelization
  −
** Automatic partition of multi-sample jobs
  −
** Reliable and fault-tolerant parallelization via GNU make
  −
*** Restart from where it stopped upon unexpected crash
  −
* Cloud & Cluster-friendly
  −
** Supports multiple clusters such as MOSIX, Slurm, & SGE
  −
** Amazon instances allow running large-scale jobs without having your own cluster
  −
  −
Sequence Processing Recommendations
  −
* Be consistent within a project
  −
** Process all samples with same pipeline
  −
*** Batch effect may arise if different pipelines are used due to pipeline differences
  −
** Use the same configuration within a project
  −
  −
== Examining GotCloud Align Input Files ==
  −
=== Sequence Data Files : FASTQs ===
  −
We already looked at those in: [[#Examining Raw Sequence Reads|Examining Raw Sequence Reads]]
      
=== Reference Files ===
 
=== Reference Files ===
−
Reference files can be downloaded with GotCloud or from other sources
+
Reference files can be downloaded with [[GotCloud]] or from other sources
 
* See [[GotCloud: Genetic Reference and Resource Files]] for more information on downloading/generating reference files
 
* See [[GotCloud: Genetic Reference and Resource Files]] for more information on downloading/generating reference files
   Line 134: Line 148:     
Take a look at the chromosome 22 reference files included for this tutorial:
 
Take a look at the chromosome 22 reference files included for this tutorial:
−
  ls ${REF}
+
  ls ${SS}/ref22
    
<ul>
 
<ul>
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<li>View Screenshot</li>
 
<li>View Screenshot</li>
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
[[File:RefDir.png|500px]]
+
[[File:RefDir.png|700px]]
 
</div>
 
</div>
 
</div>
 
</div>
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Let's read the reference FASTA file (all reference bases for the chromosome):
 
Let's read the reference FASTA file (all reference bases for the chromosome):
−
  less ${REF}/human.g1k.v37.chr22.fa
+
  less ${SS}/ref22/human.g1k.v37.chr22.fa
 +
 
 +
Remember, use <code>'q'</code> to exit out of <code>less</code>
 +
q
    
; Where is the reference sequence?
 
; Where is the reference sequence?
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<li>The ends of a chromosome are 'N' - unknown bases</li>
 
<li>The ends of a chromosome are 'N' - unknown bases</li>
 
<li>Let's look at 5 lines of the file starting at line 300,000</li>
 
<li>Let's look at 5 lines of the file starting at line 300,000</li>
−
   tail -n+300000 ${REF}/human.g1k.v37.chr22.fa |head -n 5
+
   tail -n+300000 ${SS}/ref22/human.g1k.v37.chr22.fa |head -n 5
 
[[File:Fasta.png|500px]]
 
[[File:Fasta.png|500px]]
 
</div>
 
</div>
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</ul>
 
</ul>
 
</ul>
 
</ul>
 +
 +
If you want to access the FASTA file by position, you can use <code>samtools faidx</code> command
 +
${GC}/bin/samtools faidx ${SS}/ref22/human.g1k.v37.chr22.fa 22:36000000 | less
 +
or
 +
${GC}/bin/samtools faidx ${SS}/ref22/human.g1k.v37.chr22.fa 22:36000000-36000100
    
=== GotCloud FASTQ Index File ===
 
=== GotCloud FASTQ Index File ===
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Let's look a look at the index file I prepared for this tutorial:
 
Let's look a look at the index file I prepared for this tutorial:
−
  less -S ${IN}/align.index  
+
  less -S ${SS}/align.index  
 +
 
 +
Remember, use <code>'q'</code> to exit out of <code>less</code>
 +
q
   −
; Which samples had multiple Runs?
+
; Which samples had multiple runs?
 
<ul>
 
<ul>
 
<div class="mw-collapsible mw-collapsed" style="width:500px">
 
<div class="mw-collapsible mw-collapsed" style="width:500px">
 
<li>Need a reminder of the format?</li>
 
<li>Need a reminder of the format?</li>
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
[[File:fqindex.png|650px]]
+
[[File:fqindex.png|750px]]
 +
</div>
 +
</div>
 +
<ul>
 +
<li>Note: in the screenshots, the fields are shifted into clear columns to make it easier to read</li>
 +
<ul>
 +
<li>When you view the file, the fields will not line up in neat columns and it can be hard to read</li>
 +
</ul>
 +
</ul>
 +
<div class="mw-collapsible mw-collapsed" style="width:500px">
 +
<li>Hard to read the index?  Need a hint?</li>
 +
<div class="mw-collapsible-content">
 +
<ul>
 +
<li>Use cut to extract just the MERGE_NAME & RGID fields </li>
 +
cut -f 1,4 ${SS}/align.index
 +
</ul>
 
</div>
 
</div>
 
</div>
 
</div>
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<li>HG00553 & HG00640</li>
 
<li>HG00553 & HG00640</li>
 
<li>They have multiple unique values in the RGID field</li>
 
<li>They have multiple unique values in the RGID field</li>
−
[[File:fqindexRG.png|650px]]
+
[[File:fqindexRG.png|800px]]
 
</div>
 
</div>
 
</div>
 
</div>
Line 202: Line 242:       −
How do you point Gotcloud to your index file?
+
How do you point GotCloud to your index file?
 
* Command-line <code>--index_file</code> option
 
* Command-line <code>--index_file</code> option
 
: or
 
: or
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** Most values should be left as the defaults
 
** Most values should be left as the defaults
 
* Specify values in your configuration file as:
 
* Specify values in your configuration file as:
−
KEY = value
+
** <code>KEY = value</code>
 
* Use $(KEY) to refer to another key's value
 
* Use $(KEY) to refer to another key's value
 
* If a KEY is specified twice, the later value is used
 
* If a KEY is specified twice, the later value is used
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Let's look at the configuration file I created for this test:
 
Let's look at the configuration file I created for this test:
−
  more ${IN}/gotcloud.conf
+
  more ${SS}/gotcloud.conf
 +
 
 +
Use the <code>space bar</code> to advance if the whole file isn't displayed.
   −
; If your input/reference are at a different path, what would you change?
+
; If your references are in a different path than what is specified, what would you change?
 
<ul>
 
<ul>
−
<div class="mw-collapsible mw-collapsed" style="width:200px">
+
<div class="mw-collapsible mw-collapsed" style="width:300px">
 
<li>Answer:</li>
 
<li>Answer:</li>
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 
<ul>
 
<ul>
−
<li>Change <code>IN_DIR</code> & <code>REF_DIR</code></li>
+
<li>You would change <code>REF_DIR</code> to the new path</li>
−
[[File:gcConf.png|500px]]
+
[[File:gcConf.png|800px]]
 
</div>
 
</div>
 
</div>
 
</div>
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</ul>
 
</ul>
   −
== Run GotCloud Align ==
+
== Run [[GotCloud]] Align ==
 +
 
 +
[[File:AlignDiagram.png|500px]]
 +
 
 
Now that we have all of our input files, we need just a simple command to run them
 
Now that we have all of our input files, we need just a simple command to run them
−
  ${GC}/gotcloud align --conf ${IN}/gotcloud.conf --numcs 2
+
  ${GC}/gotcloud align --conf ${SS}/gotcloud.conf --numcs 2 --base_prefix ${SS} --outdir ${OUT}
 +
 
 +
* <code>${GC}/gotcloud</code> runs GotCloud
 +
* <code>align</code> tells GotCloud you want to run the alignment pipeline.
 +
* <code>--conf</code> tells GotCloud the name of the configuration file to use.
 +
** The configuration for this test was downloaded with the seqshop input files.
 
* <code>--numcs</code> means to run 2 samples at a time.
 
* <code>--numcs</code> means to run 2 samples at a time.
−
** How many you can run concurrently depends on your system
+
** How many you can run concurrently depends on your system.
 +
* <code>--base_prefix</code> tells GotCloud the prefix to append to relative paths.
 +
** The Configuration file cannot read environment variables, so we need to tell GotCloud the path to the input files, ${SS}
 +
** Alternatively, gotcloud.conf could be updated to specify the full paths
 +
* <code>--out_dir</code> tells GotCloud where to write the output.
 +
** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line
 +
 
 
[[File:gcalignStart.png|850px]]
 
[[File:gcalignStart.png|850px]]
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If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off.
 
If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off.
 +
 +
Inside GotCloud align, not only sequence alignment but also pre-processing of sequence data, including deduplication and base quality recalibration are performed along with quality assessment, as illustrated below.
 +
 +
[[File:Gotcloud_align_detail.png|500px]]
    
== Examining GotCloud Align Output ==
 
== Examining GotCloud Align Output ==
    
Let's look at the output directory:
 
Let's look at the output directory:
−
  ls ${OUTPUT}
+
  ls ${OUT}
 
[[File:gcalignOutM.png|600px]]
 
[[File:gcalignOutM.png|600px]]
   −
Let's look at the BAMs (aligned reads that are ready for variant calling):
+
=== Quality Control Files ===
−
ls ${OUTPUT}/bams
  −
[[File:GcalignOutBAMm.png|600px]]
  −
 
  −
BAM Files:
  −
* Binary Sequence Alignment/Map (SAM) Format
  −
* Maps reads to Chromosome/Position
  −
* For a detailed explanation of the SAM/BAM format, see:
  −
** SAM/BAM Spec: http://samtools.github.io/hts-specs/SAMv1.pdf
  −
** Additional information I put together as I started working with SAM/BAM: [[SAM]]
  −
* Consists of:
  −
** Header
  −
*** Starts with '@'
  −
*** Records - one for each sequence read
  −
Let's examine a BAM file:
  −
samtools view -h ${OUTPUT}/bams/
  −
[[File:BAM.png|750px]]
  −
 
   
Let's take a look at our quality control output directory:
 
Let's take a look at our quality control output directory:
−
  ls ${OUTPUT}/QCFiles  
+
  ls ${OUT}/QCFiles  
 
[[File:GcalignOutQCm.png|600px]]
 
[[File:GcalignOutQCm.png|600px]]
    +
==== Sample Contamination/Swap ====
 
Check for sample contamination:
 
Check for sample contamination:
 
* *.selfSM : Main output file containing the contamination estimate.  
 
* *.selfSM : Main output file containing the contamination estimate.  
−
** If you are only interested in checking sample contamination:
+
** Check the 'FREEMIX' column for genotype-free estimate of contamination
−
*** Check the 'FREEMIX' column for genotype-free estimate of contamination
   
**** 0-1 scale, the lower, the better
 
**** 0-1 scale, the lower, the better
−
**** See [[VerifyBamID#A_guideline_to_interpret_output_files|VerifyBamID: A guideline to interpret output files]] for more information
+
**** If [FREEMIX] >= 0.03 and [FREELK1]-[FREELK0] is large, possible contamination
−
*** Check the 'CHIPMIX' column for contamination estimates with external genotypes (if provided)
+
** See [[VerifyBamID#A_guideline_to_interpret_output_files|VerifyBamID: A guideline to interpret output files]] for more information
−
* *.selfRG : Same output to .*selfSM, but separated by readGroup (which might be helpful for library-level examination)
+
  less -S ${OUT}/QCFiles/HG00551.genoCheck.selfSM
−
* *.depthSM : depth distribution of reads covering the marker position of the input VCF, across all readGroups.
+
 
−
* *.depthRG : depth distribution of reads covering the marker position of the input VCF, per readGroups.
+
Remember, use <code>'q'</code> to exit out of <code>less</code>
−
  less -S ${OUTPUT}/QCFiles/HG00551.genoCheck.selfSM
+
q
 +
 
 +
; Is there evidence of sample contamination?
 +
<ul>
 +
<div class="mw-collapsible mw-collapsed" style="width:200px">
 +
<li>Answer:</li>
 +
<div class="mw-collapsible-content">
 +
<ul>
 +
<li>No, FREEMIX = 0.00000 (<0.03)</li>
 +
</ul>
 
[[File:Contam1.png|700px]]
 
[[File:Contam1.png|700px]]
 +
</div>
 +
</div>
 +
</ul>
 +
 +
==== QC Metrics ====
 +
See: [[QPLOT#Diagnose_sequencing_quality|QPLOT: Diagnose sequencing quality]] for more info on how to use QPLOT results.
   −
Next, let's look at some quality control metrics:
+
Let's look at some quality control metrics:
−
  cat ${OUTPUT}/QCFiles/HG00551.qplot.stats
+
  cat ${OUT}/QCFiles/HG00551.qplot.stats
−
* 99.16% mapping rate
  −
* 94.01% high quality bases
  −
* 7x coverage
  −
* 31.3% A, 31.3% T
  −
* 18.7% C, 18.7% G
      +
; What is the mapping rate & average coverage for HG00551?
 +
<ul>
 +
<div class="mw-collapsible mw-collapsed" style="width:200px">
 +
<li>Answer</li>
 +
<div class="mw-collapsible-content">
 +
<ul>
 +
<li> 98.93% Mapped</li>
 +
<li>7.43 MeanDepth</li>
 +
</ul>
 +
[[File:qplots.png|200px]]
 +
</div>
 +
</div>
 +
</ul>
   −
Generate the pdf's of our quality metrics:
+
Generate a pdf of quality metrics:
−
  Rscript ${OUTPUT}/QCFiles/HG00551.qplot.R
+
  Rscript ${OUT}/QCFiles/HG00551.qplot.R
−
Rscript ${OUTPUT}/QCFiles/HG00553.qplot.R
  −
Rscript ${OUTPUT}/QCFiles/HG00640.qplot.R
  −
Rscript ${OUTPUT}/QCFiles/HG00641.qplot.R
      
Examine the PDF:
 
Examine the PDF:
−
  evince  ${OUTPUT}/QCFiles/HG00551.qplot.pdf&
+
  evince  ${OUT}/QCFiles/HG00551.qplot.pdf&
−
The first plot: Empirical vs reported Phred score does not look as good as we would like.
+
 
−
* This is due to the small region used for recalibration
+
It is ok if you see a warning message when opening evince.  It should still open.  If not, let me know.  To close evince, just close the pdf window.
−
Look at the PDF I produced when I ran the whole genome:
+
 
−
  evince ${GC}/example/HG00551.wg.qplot.pdf&
+
;Does the Empirical vs reported Phred score look as good as we would like?
 +
<ul>
 +
<div class="mw-collapsible mw-collapsed" style="width:400px">
 +
<li>Answer</li>
 +
<div class="mw-collapsible-content">
 +
<ul>
 +
<li> No, it is well above the line</li>
 +
<li> This is due to the small region used for recalibration</li>
 +
[[File:Qplotpdf.png|400px]]
 +
<li> Look at the PDF I produced when I ran the whole genome:</li>
 +
  evince ${SS}/ext/HG00551.wg.qplot.pdf&
 +
</ul>
 +
[[File:Qplotpdfwg.png|400px]]
 +
</div>
 +
</div>
 +
</ul>
 +
 
 +
=== BAM Files ===
 +
Binary Sequence Alignment/Map (SAM) Format
 +
* Maps reads to Chromosome/Position
 +
* For a detailed explanation of the SAM/BAM format, see:
 +
** SAM/BAM Spec: http://samtools.github.io/hts-specs/SAMv1.pdf
 +
** Additional information I put together as I started working with SAM/BAM: [[SAM]]
 +
 
 +
Let's look at the BAMs (aligned reads that are ready for variant calling):
 +
ls ${OUT}/bams
 +
[[File:GcalignOutBAMm.png|600px]]
 +
 
 +
Let's examine at the first 5 lines of the BAM file using [http://samtools.sourceforge.net/samtools.shtml#3 samtools view]:
 +
${GC}/bin/samtools view -h ${OUT}/bams/HG00551.recal.bam|head -n 5
   −
See: [[QPLOT#Diagnose_sequencing_quality|QPLOT: Diagnose sequencing quality]] for more info on how to use QPLOT results.
+
; What are the chromosome and position of the first record in the BAM file?
 +
<ul>
 +
<div class="mw-collapsible mw-collapsed" style="width:300px">
 +
<li>Need a reminder of the format?</li>
 +
<div class="mw-collapsible-content">
 +
[[File:Bam.png|750px]]
 +
</div>
 +
</div>
 +
<div class="mw-collapsible mw-collapsed" style="width:300px">
 +
<li>Answer</li>
 +
<div class="mw-collapsible-content">
 +
<ul>
 +
<li>Chr 22, Pos: 16114122</li>
 +
</ul>
 +
[[File:BamRec.png|650px]]
 +
</div>
 +
</div>
 +
</ul>
 +
 
 +
==== Accessing BAMs by Position ====
 +
BAM's are so big, what if we want to see a position part way through the file?
 +
*[http://samtools.sourceforge.net/samtools.shtml#3 samtools] has an option for that.
 +
 
 +
Add a region to the view command we used above.  Let's find all reads that overlap positions 36907000-36907005:
 +
${GC}/bin/samtools view -h ${OUT}/bams/HG00551.recal.bam 22:36907000-36907005
 +
* Just a few reads.
 +
 
 +
Let's visualize what reads in that area look like using samtools tview:
 +
${GC}/bin/samtools tview ${OUT}/bams/HG00551.recal.bam ${SS}/ref22/human.g1k.v37.chr22.fa
 +
* Type ‘g’
 +
** Type 22:36907000
 +
* Type ‘n’ to color by nucleotide
 +
* Use the arrow keys to move around and look at the area.
 +
 
 +
Understanding the syntax:
 +
* '.' : match to the reference on the forward strand
 +
* ',' : match to the reference on the reverse strand
 +
* ACGTN : mismatch to reference on the forward strand
 +
* acgtn : mismatch to reference on the reverse strand
 +
 
 +
; Do you see anything interesting?
 +
<ul>
 +
<div class="mw-collapsible mw-collapsed" style="width:500px">
 +
<li>Screenshot</li>
 +
<div class="mw-collapsible-content">
 +
<ul>
 +
<li>We will have to remember this region when we run snpcall to see what it says.</li>
 +
</ul>
 +
[[File:tview.png|750px]]
 +
</div>
 +
</div>
 +
</ul>
 +
 
 +
Other tview commands:
 +
* Type '?' for a help screen
 +
* Type 'q' to quit tview
 +
 
 +
Feel free to play around more and browse the BAM files.
 +
 
 +
==== Other tools for BAMs ====
 +
We have developed a lot of tools that operate on BAM files.
 +
 
 +
See [[Software#BAM_Util_Tools|Software: BamUtil Tools]] for a list
 +
* Many operations:
 +
** diff : diff 2 BAM files
 +
** stats: per positions statistics
 +
** bam2Fastq : convert a BAM back to a FASTQ (how I created the fastqs for this tutorial)
 +
** Lots of others
 +
* Feel free to try some out
 +
* If you have any questions, let me know, I wrote most of them and am happy to help.
 +
 
 +
== Logging Off ==
 +
 
 +
''This section is specifically for the SeqShop Workshop computers.''
 +
<div class="mw-collapsible mw-collapsed" style="width:600px">
 +
''If you are not running during the SeqShop Workshop, please skip this section.''
 +
<div class="mw-collapsible-content">
 +
To logout of seqshop-server, type:
 +
exit
 +
And close the windows.
 +
 
 +
When done, log out of the Windows machine.
 +
</div>
 +
</div>
Ppwhite
96

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