Question: Bin blast results into hit vs. no-hit
gravatar for jaydu
13 months ago by
jaydu0 wrote:

Hi there,

Geneious has the wonderful possibility to sort blast hits into two bins, hit or no-hit. This is quite useful to i.e. separate metagenomes (i.e. host reads vs. endosymbiont reads). While Geneious works very well with smaller data-sets on a local computer, for large data-sets you need a lot of patience. Is there any way to use a command line blast in the same way so one ends up with two files with the sequence IDs or even better two files with hit vs no-hit sequences? There is no need at all to produce all that alignments.

I thought about a similar approach with BBMap, but because in our case there is no reference genome from the same species blasting the hits against a somewhat related genome might be the better approach.

Thank you for your help, JD

blast • 270 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by jaydu0

You can post-process your blast results if you use -outfmt 7. That will include queries with no hits in your output. If you use outfmt 6 then that will include only those query ID's that have hits. You could use those to find ones that don't that way.

With BBMap you can collect reads that don't align by using outu= option.

ADD REPLYlink written 13 months ago by genomax85k
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