Open songtaogui opened 4 years ago
Hello,
Thank you very much for your interest in T-lex3.
It is ok if you want to modify it to skip BWA MEM, but notice that fastq files are still needed for the Absent module (which uses a different mapper).
Let us know if we can help with any issue.
Thank you.
María
Hi,
Thank you for this wonderful program.
I have noticed that in the T-lex3 pipeline, the reads were mapped to ref with BWA MEM using default options. So I was wondering that is it OK if I modified the script to skip the BWA MEM step by providing a pre-build bwa-mem.bam file? In that case, should I still provide the reads.fastq? (If the reads.fastq files were only used for bwa mapping, I would like to modify the script to get rid of these options, because I have removed my raw reads.fq after bwa mapping)
Any suggestion would be grateful.
Best wishes,
SongtaoGui