I had a question about best practices regarding adaptor removing, trimming the ends of reads, and also removing short reads. All of these questions pertain preparing sequences for alignment with BWA.
1) Adaptor removal: we can either mask the adapter with Casava (puts N's) or clip it out with cutadapt, what is the best practice (masking vs. removing) for BWA?
2) Trimming at the ends: I have heard that this is important, trim a few bases at the beginning and also at the end (say 10 and 10). We can also just mask it with Casava, or trim it with some program. What is a standard program for trimming ends of reads?
3) Removal of short reads: when clipping out the adapter, sometimes this results in a few very small reads (ligated adapters perhaps), those small reads seem to give problems to BWA, we wrote a program for removing small reads but it is slow, is there any software out there that does it?
Thanks in advance,
Ramiro
1) Adaptor removal: we can either mask the adapter with Casava (puts N's) or clip it out with cutadapt, what is the best practice (masking vs. removing) for BWA?
2) Trimming at the ends: I have heard that this is important, trim a few bases at the beginning and also at the end (say 10 and 10). We can also just mask it with Casava, or trim it with some program. What is a standard program for trimming ends of reads?
3) Removal of short reads: when clipping out the adapter, sometimes this results in a few very small reads (ligated adapters perhaps), those small reads seem to give problems to BWA, we wrote a program for removing small reads but it is slow, is there any software out there that does it?
Thanks in advance,
Ramiro
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