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Revision as of 16:02, 25 June 2014
, 16:02, 25 June 2014→Examining GotCloud Align Input Files
* 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.
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
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>
Remember, use <code>'q'</code> to exit out of <code>less</code>
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>
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>
Remember, use <code>'q'</code> to exit out of <code>less</code>
If you want to access the FASTA file by position, you can use <code>samtools faidx</code> command
If you want to access the FASTA file by position, you can use <code>samtools faidx</code> command
$GC/bin/samtools faidx $REF/human.g1k.v37.chr22.fa 22:36000000 | less
${GC}/bin/samtools faidx ${SS}/ref22/human.g1k.v37.chr22.fa 22:36000000 | less
or
or
$GC/bin/samtools faidx $REF/human.g1k.v37.chr22.fa 22:36000000-36000100
${GC}/bin/samtools faidx ${SS}/ref22/human.g1k.v37.chr22.fa 22:36000000-36000100
; Where is the reference sequence?
; Where is the reference sequence?
<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]]
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