Question: small FASTa file from genome guided trinity assembly?
0
gravatar for bsly
3 days ago by
bsly0
bsly0 wrote:

Hello,

I have run Genome Guided Trinity with RSEM data from RNAseq of my organism and a closely related reference. Despite getting about 13,000 identified genes with RSEM, my FASTa file from ggTrinity only contains about 30 genes of short length. Any ideas of why this might be are greatly appreciated!

Thanks, Belinda

ADD COMMENTlink written 3 days ago by bsly0

Any code/ commands you can paste from your Trinity run?

Trinity uses fastq and outputs fasta. You then use your fastq reads and count the read alignments with RSEM. So I'm not sure why you are running RSEM data in Trinity...?? Do you mean you used a particular Trinity pipeline rather than the assembly Trinity.pl script?

Do a: grep -c '>' X with X being the name of your fasta file. Report back.

ADD REPLYlink written 3 days ago by Biogeek310
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1625 users visited in the last hour