How to reduce the size of blastall output

Question

[Ric]

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.

Answer 1

[Asaf]

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.

[Ric]

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

[Asaf]

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

[Ric]

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

[Asaf]

Then you should take only the best match I think