Percent identity threshold?

Open schwarl opened this issue 6 years ago • 1 comments

Hi! I am having some trouble filtering my RNASeq reads. I have a lot of mitochondrial rRNA that I want to get rid of, but I can't seem to manage that without also filtering out a lot of mitochondrial coding sequences. I tried using a custom fasta file with the 12S and 16S sequences from my study organisms, and end up with a lot of low identity, but low e-value matches to CO1 or NADH sequences from unrelated taxa (I assume because my fasta file only has 8 sequences in it). Is there a way to filter by percent identity rather than e-value? Thanks so much!

Feb 06 '20 17:02 schwarl

@schwarl Hi, %id currently cannot be filtered using a convenient option. However, if you generate the Blast report using e.g. --blast 1 option, you can review the %id (3rd column 78.9 below)

DRR121111.1.1	EU602318	78.9	127	22	5	1	127	28	151	7.32e-17	97

Feb 06 '20 19:02 biocodz