BWA option about the insert size

Question

[xieduo9394]

Hi,

I am using BWA to do alignment and estimate the insert size of my data and the excepted insert size length is 2000bp,so I use the "sampe" command to do alignment,but I found "-a" option is available,and the description of this option is:

Maximum insert size for a read pair to be considered being mapped properly. Since 0.4.5, this option is only used when there are not enough good alignment to infer the distribution of insert sizes. [500]

I use this option and set it to "-a 2000", but I don't know clearly what impact will this option have on my result?Should I use this option?

Thanks.

[GenoMax]

If this is standard illumina sequencing it is unlikely that your inserts are 2kb in size. If you have a reference available you can easily figure out the insert size using bbmap.sh from BBMap suite. bbmap.sh ref=ref.fasta in1=r1.fq in2=r2.fq ihist=ihist.txt

[bruce.moran]

Without reference, and much faster, is BBMerge (what a surprise that it's part of BBMap!), with a little command line addition to catch output in a text file and allow it to be output to screen also:

bbmerge.sh in1=r1.fq in2=r2.fq out=merged.fq 2>&1 | tee insert.txt

[GenoMax]

This will only work when there are reads (I am not sure how many need to) that overlap.