Changes

*Flag filter

*Flag filter

By default all reads are processed. If it is desired to check only the first read of a pair, use --read2_skip to ignore the second read. And so on.

** By default reads marked as dup and QCFile are ignored but can be retained by

--dup_keep or --qcfail_keep

*Records to process is to try the first n reads to test the bam files and check whether it works.

 

 

*Records to process  

This option will enable qplot to read the first '''n''' reads to test the bam files and check whether it works.

* Lanes to process

* Lanes to process

** If the input bam files have more than one lane and only some of them need to be checked, they can be specified by --lanes 1,3,5 whatever the number of lanes needed.

 

** In order for this to work, the lane info has to be encoded in the read name such that lane number is the second field with the delimit of ":".

If the input bam files have more than one lane and only some of them need to be checked, they can be specified by --lanes 1,3,5 whatever the number of lanes needed.

 

'''NOTE''' In order for this to work, the lane info has to be encoded in the read name such that lane number is the second field with the delimit of ":".

* Region list

* Region list

** If the interest of QA is a list of regions, e.g. exons, this can be achieved by providing a list of region. The regions should be in the form of "chr start end label" each line in the file. In order for this option to work, within each chromosome (contig) the regions have to be sorted by starting position, and also the input bam files have to be sorted.  

 

If the interest of qplot is a list of regions, e.g. exons, this can be achieved by providing a list of region. The regions should be in the form of "chr start end label" each line in the file. In order for this option to work, within each chromosome (contig) the regions have to be sorted by starting position, and also the input bam files have to be sorted.  

  1 100 500 region_A

  1 100 500 region_A

  1 600 800 region_B

  1 600 800 region_B

* Plot labels

* Plot labels

** Two kinds of labels are enabled. First one is the label for the plot (default is empty), e.g. label on the title of each subplot. Second one is a set of labels for each input bam files, e.g. sample ID (default is numbers 1, 2, ... until the number of input bam files.

 

Two kinds of labels are enabled. First one is the label for the plot (default is empty), e.g. label on the title of each subplot. Second one is a set of labels for each input bam files, e.g. sample ID (default is numbers 1, 2, ... until the number of input bam files. For example:

  --label Run100 --bamLabels s1,s2,s3,s4,s5,s6,s7,s8

  --label Run100 --bamLabels s1,s2,s3,s4,s5,s6,s7,s8

* Multiple threading

* Multiple threading (not officially supported)

** Number of concurrent threads running for the input bam files. One bam file will be processed by one thread. Therefore using a number which is dividable by the number of input bam files will make it efficient. One extra thread requires memory about 375Mb on top of around 4Gb memory used to hold reference and GC content file.

 

Number of concurrent threads running for the input bam files. One bam file will be processed by one thread. Therefore using a number which is dividable by the number of input bam files will make it efficient. One extra thread requires memory about 375Mb on top of around 4Gb memory used to hold reference and GC content file.

== Output files ==

== Output files ==