Shorten Illumina reads

Question

[kirillkirilenko]

I have a somewhat unusual question: I want to change the paired-end read size from 150 bases to 101 bases for the entire library. I am working with RepeatExplorer2 in protocol-2 (Comparative analysis) mode, and it requires the same read length for all libraries. However, one of my libraries is 101 bases in size while the others are 150 bases. I believe I need to remove 49 bases from the left part of R1 read and 49 bases from the right part of R2, is that correct?

Answer 1

[Brian Bushnell]

No, you need to remove 49 bases from the right end of read 1 and read 2. Using BBTools, the command would be:

reformat.sh in1=r1.fq in2=r2.fq out1=trimmed1.fq out2=trimmed2.fq ftr2=100

It's safer to "trim to at most 101bp", which that command does, instead of "trim the last 49 bases" (the flag for that would be "ftr=49") in case you are operating on already-trimmed reads of variable length. If you had trimmed the left side of R1, you would get lower overall quality and a different insert size distribution from the other libraries.