hey everyone,
I am looking into a SAM file now and found the MAPQ field all filled with 255. 255 means mapping quality not available, right? So I want to use bowtie to remap the tags in Fastq format, and hopefully get the mapping quality scores instead of 255.
My question is, with bowtie, how to calculate the MAPQ for each tag? I have read the bowtie manual and got no clue at all... If I use "--MAPQ <int>", that means I set the quality by myself. But I don't know it. Shouldn't bowtie be able to calculate quality scores for each tag based on the fastq file??
Thanks for your help in advance!
I am looking into a SAM file now and found the MAPQ field all filled with 255. 255 means mapping quality not available, right? So I want to use bowtie to remap the tags in Fastq format, and hopefully get the mapping quality scores instead of 255.
My question is, with bowtie, how to calculate the MAPQ for each tag? I have read the bowtie manual and got no clue at all... If I use "--MAPQ <int>", that means I set the quality by myself. But I don't know it. Shouldn't bowtie be able to calculate quality scores for each tag based on the fastq file??
Thanks for your help in advance!
Comment