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How to reduce the size of blastall output

Hi, I am running blastall -p blastn -i ${i} -d ${db} -F F -e 1e-10 -E -1 -v 20000 -b 20000 -a 1 -K 1 > output/${output}.blast and I just wondering how could I even further to reduce the output file size by e.g. reducing the number of hits?

Thank you in advance.

blast
• 2,080 views • link
updated by Asaf Asaf • written by Ric Ric

1 answer

  1. You can output in tabular format (-m 8)

  2. You can gzip it on the fly:

    blastall -p blastn -i ${i} -d ${db} -F F -e 1e-10 -E -1 -v 20000 -b 20000 -a 1 -K 1 |gzip -c > output/${output}.blast

  3. You use high values of -b and -v, you can reduce them if you want less hits.

• 0 views • link
written by Asaf Asaf

What would be the best values for -b and -v? I need to plot a circos plot.

• 0 views • link
written by Ric Ric

It all depends of the question you ask (rather than the way of presenting the results)

• 0 views • link
written by Asaf Asaf

I trying to plot synteny plots between a reference genome which has chromosomes and a new contig based assembly.

• 0 views • link
written by Ric Ric

Then you should take only the best match I think

• 0 views • link
written by Asaf Asaf

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