Question: Do the lowercase bases seen in BAM files need to be reverse complemented in consensus?
gravatar for DNAngel
9 months ago by
DNAngel40 wrote:

I'm creating consensus sequences using a custom script but I am unsure if lowercase bases (the bases that are on the reverse strand) are already reverse complemented, or they need to be reverse complemented?

In IGV, when I see reads aligned to a position and I have a mix of A (forward reads), and 'a' (reverse reads) from single-end data, can I assume that 'a' is already reverse complemented where the reverse read actually had a 'T' at that position? Or will I have to account for this myself and really I have 'A' and 'T' matched at that position?

Thank you!

bam • 278 views
ADD COMMENTlink modified 9 months ago by Devon Ryan92k • written 9 months ago by DNAngel40
gravatar for Devon Ryan
9 months ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

All alignments in a BAM file are written for the + strand, so they've been reverse complemented as appropriate. IGV is just indicating their orientation with upper/lower case letters, you don't need to do anything else yourself in that regard.

Whether a reverse complemented read actually arose from the - strand will end up being library type dependent, in case you're wondering about that as well.

ADD COMMENTlink written 9 months ago by Devon Ryan92k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1116 users visited in the last hour