Sam quality flag

[unique379]

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 its 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

[dpryan]

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.