Extract cds sequence from RNA reads mapped to ref genome?

Question

[nute11a]

Hello!

I used STAR to map my RNA reads to a reference genome. I am now interested in extracting the sequence for gene X.

I tried to convert the bam file to fasta, but it didn't seem to give me a consensus sequence. I also used Trinity ref-assemble to get the cds sequences, which I used Transdecoder to get the pep sequences. I was thinking about trying to BLAST these against the X- ref genome sequence, but surely there is a way to get this through mapping?

I looked into this: How To Extract Full Sequence Of A Gene From Bam Or Sam File but it appears to be for VCF files.

I appreciate your help!

[Jesse]

That's the one approach I'm aware of too (use variant calls plus reference to get consensus) but you could generate a VCF from your BAM in order to use that method, right?

Here's a similar example using bcftools consensus instead of vcfutils.pl, but it's the same basic idea as what you linked: https://samtools.github.io/bcftools/howtos/consensus-sequence.html. I'm not attempting to write an answer here since I'm not 100% sure on these methods myself though.