Apologies if this has been asked before.
I'm quite familiar with Bowtie, which I use with the following options:
--best --strata -m 1
To retrieve only "uniquely" mapping chip-seq reads. On completion of an alignment, Bowtie provides an output similar to this:
# reads processed: 2307803
# reads with at least one reported alignment: 1653076 (71.63%)
# reads that failed to align: 236689 (10.26%)
# reads with alignments suppressed due to -m: 418038 (18.11%)
Reported 1653076 alignments to 1 output stream(s)
Where I interpret that 71.63% as the number of uniquely mapping reads.
Now I would like to do the same with BWA. I have ran BWA with default options and would like to generate similar statistics. Is there a tool that allows me to do that? I understand that, having used default options, I will have "multiply" mapping reads, but these reads are given a MAPQ=0 by bwa.
Any suggestions would be appreciated. Thanks!
I'm quite familiar with Bowtie, which I use with the following options:
--best --strata -m 1
To retrieve only "uniquely" mapping chip-seq reads. On completion of an alignment, Bowtie provides an output similar to this:
# reads processed: 2307803
# reads with at least one reported alignment: 1653076 (71.63%)
# reads that failed to align: 236689 (10.26%)
# reads with alignments suppressed due to -m: 418038 (18.11%)
Reported 1653076 alignments to 1 output stream(s)
Where I interpret that 71.63% as the number of uniquely mapping reads.
Now I would like to do the same with BWA. I have ran BWA with default options and would like to generate similar statistics. Is there a tool that allows me to do that? I understand that, having used default options, I will have "multiply" mapping reads, but these reads are given a MAPQ=0 by bwa.
Any suggestions would be appreciated. Thanks!
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