Is there a way to make the BLAST results easier to read?
Entering edit mode
4 weeks ago
Riku ▴ 60

Hi all.

I'm trying to get assembly stat. As part of that, I would like to evaluate the assembly quality by running BLAST to the fasta file output by Trinity. I got the result by blastx, but it is difficult to evaluate the result. Is there any way to evaluate the result of each sequence at once?

I'm referring to table S1 in this paper.

I'm very appriciate for your help!

RNA-seq BLAST Trinity • 249 views
Entering edit mode

The BIRCH system presents BLAST output in 3 different ways: the HTML report, using BlastViewer, and in a tabular form using BioLegato, which is shown here: BLAST output in blnfetch. The table can be sorted on any combination of columns, ascending or descending, so in this case you'd want to sort on column C, the species names. BIRCH has an extensive collection of programs for genomics tasks, including by the way Trinity. You can see these in action on the BIRCH YouTube channel.

Entering edit mode
4 weeks ago

To easily generate the count table, you could do the following. Use tabular output in local blast: -outfmt "6 staxid ssciname" then count occurrences by piping into | sort | uniq -c like so:

blastx -db nr -query Trinity.fasta -evalue 1e-6 -outfmt "6 staxid ssciname" | sort | uniq -c | sort -n > taxon-counts.txt

You may want to adjust parameters, also whether or not staxid and ssciname work depend on how the database was built.


Login before adding your answer.

Traffic: 2575 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6