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Old 05-27-2014, 05:21 AM   #46
Location: Germany

Join Date: Jan 2014
Posts: 39

Hey Brian,

i just briefly checked BBMap and have some questions.

1) I am working, among others, with RNA-Seq data of a cyanobacterium. Is it possible that BBMap performs a spliced alignments for my RNA-Seq data? In a small run i did not observed spliced alignments but nevertheless i was wondering about it. If so, can i prevent this case by setting 'intronlen' to 0?

2) Is there a way to apply soft- or hard-clipping?
For example bwa performs for a read soft-clipping leading to 94M6S where BBMap leads to 100M although the last 6 bases are partially mismatches and therefor i want them to be clipped.

3) Is there a way to determine the maximal number of mismatches?

4) For CRAC and PAR-Clip sequencing data i want only 1 respectively 2 mismatches/indels. So when i want at most 2 indels i have to set maxindel= 2 and strictmaxindel = true. Am i right?

5) Does BBMap reports only the best alignment (or best alignments if alignments with equal quality are present) or is there a way to report also alignments that are not as good as the best alignment? Would this be the maxsites option?

Thanks for your nice support!

Mchicken is offline   Reply With Quote