Exctract unmapped reads from BLAST

Question

[Pilar]

Hi, I used Blast and Trinotate to annote de novo assembly I constructed using Trinity.

Now, I want to study that transcripts without blast hit (they doesn't appear in the Trinotate output). My question is: How can I exctract that unmapped transcripts? Is there a way to tell blast to output the unmapped reads into a separate file?

I want do it because I'm studdying the presence of new Antimicrobial Peptide Genes in Blatella germanica (it doesn't have a reference genome).

Any advice or suggestion is welcome. Thanks in advance :)

Answer 1

[GenoMax]

Is there a way to tell blast to output the unmapped reads into a separate file?

No there is not. You will need to use -outfmt 7 when you blast (which will include reads that do not map) and then pull out the id's of the reads that do not map. See: Blast - How to get the no hits result on table output?

Once you have the id's that do not map, you can use answer here to extract the reads from your query file: Extract fasta sequnces not matching a list

[Pilar]

Thank you very much. I've used -outfmt 7 repeating my blast step. I'm working with a huge database, so it's going to take many hours to finish. Anyway, your response has been very useful :) thank you

Answer 2

[Pierre Lindenbaum]

have a look at comm or join.

[Pilar]

Thanks for answering :), sorry, I'm new at this. These are commands I should use when I launch Blast in terminal?

[Pierre Lindenbaum]

those are two distinct commands https://linux.die.net/man/1/comm and https://linux.die.net/man/1/join

extract the names of your queries, sort and save into 'a'. extract the names of the blast output and save into 'b'

'comm -23 a b' will show you the queries that were not found by blast.

[Pilar]

Thank you very much for your quickly response. The comm command has been very useful :) I figure I have the output file I needed.