How to extract the desired fasta file from the de novo assembly Trinity fasta file

Question

[snar86]

Hi,

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.

Answer 1

[Brian Bushnell]

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:

filterbyname.sh in=trinity.fasta out=filtered.fasta names=names.txt include

[Bioinfonext]

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

Answer 2

[Antonio R. Franco]

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