Question: How to extract the desired fasta file from the de novo assembly Trinity fasta file
gravatar for snar86
4.2 years ago by
snar8610 wrote:


I have fasta file of my de novo assembly result from Trinity software. After blast, i listed the transcripts that were related to my project. Is there anyone can help me on how to get the fasta file for only the transcripts that i have listed from that de novo assembly result?

Thank you.

rna-seq sequence assembly • 1.3k views
ADD COMMENTlink modified 4.2 years ago by Antonio R. Franco4.5k • written 4.2 years ago by snar8610
gravatar for Brian Bushnell
4.2 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

If you have the names of the relevant transcripts in a text file, with one name per line, you can get them using the BBMap package like this: in=trinity.fasta out=filtered.fasta names=names.txt include
ADD COMMENTlink written 4.2 years ago by Brian Bushnell17k

Thanks Brian for wonderful software.........bbmap does multiple things for NGS analysis.

ADD REPLYlink written 3.5 years ago by Bioinfonext250
gravatar for Antonio R. Franco
4.2 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

You can also take a look to the faSomeRecords program. Think as an alternative to the previous one. The nice thing about this is that is written in C and is accompanied by a bunch of other useful programs It requires a 64bit environment, though

ADD COMMENTlink written 4.2 years ago by Antonio R. Franco4.5k
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