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Old 05-27-2014, 04:21 AM   #46
Mchicken
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Location: Germany

Join Date: Jan 2014
Posts: 39
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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
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