Sam Quality Flag

Question

[bioinforupesh2009.au]

Hello all,

heading just a quick reply

I aligned my color-space fastq by bowtie 1 and got sam as output. But in my all mapped reads I have 255 instead any quality information, that means quality information is absent. However, my question is..

1) Why it's happened? 2) Lacking this quality information would really hurt for my further analysis by this sam? (lets say DE analysis or any downstream analysis)

Thanks in advance

[brentp]

bowtie 1 reports the quality as 255 for all mapped reads. part of the reason for its speed is that it doesn't calculate mapping quality.

Answer 1

[Devon Ryan]

With bowtie1 (as with earlier versions of tophat), a MAPQ of 255 means a unique alignment. The other MAPQ scores for bowtie1 are 0, 1, 2, and 3, which indicate different levels of multiple mappings. For DE, you just care about unique alignments, so just filter by MAPQ accordingly.

BTW, this is cross-posted on seqanswers.

Edit: I should clarify that it seems that the options you give to bowtie1 affect this. If 255 is the only MAPQ, then as brentp mentioned, that just means mapped.

[bioinforupesh2009.au]

ok sir, thank you for your answer, its clear now.