Question: Filtering BLAST results.
0
gravatar for bpz
22 months ago by
bpz30
Mexico
bpz30 wrote:

Hello. I need some advice about how I can handle some BLAST results.

I have a set of Illumina reads obtained from a metagenomic sample. I need to obtain from these reads the ones belonging to a certain organism, while eliminating others. I prepared a BLAST database from the genomes (mitogenomes) of the organism I am interested in, plus 3 others I need to "screen-out". The query for the BLAST were the Illumina reads.

I have the results (in tabular output) and I need to keep the reads that are a match to my problem organism, and eliminate the ones that are also a (better) match to the other 3.

Any ideas on how can I achieve this? Thanks for your help.

 

filtering blast metagenomics • 748 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by bpz30

Show a header of your table.

ADD REPLYlink written 22 months ago by Biomonika (Noolean)2.9k

HWI-ST1379:164:c5k28acxx:3:1101:2770:2209       NC_008332.1                              100.00  89      0       0
1       89      146573  146485  1e-41    165
HWI-ST1379:164:c5k28acxx:3:1101:2770:2209       gi|40794996|gb|AY506529.1|      100.00  89      0       0       1       89      137429  137341  1e-41    165
HWI-ST1379:164:c5k28acxx:3:1101:2770:2209       gi|93116077|gb|DQ490952.1|      100.00  89      0       0       1       89      642229  642141  1e-41    165
HWI-ST1379:164:c5k28acxx:3:1101:2770:2209       gi|93116122|gb|DQ490953.1|      100.00  89      0       0       1       89      53028   52940   1e-41      165
HWI-ST1379:164:c5k28acxx:3:1101:2770:2209       NC_007982.1                                100.00  89      0       0       1       89      137429  137341  1e-41    165
HWI-ST1379:164:c5k28acxx:3:1101:2770:2209       gi|102567891|gb|DQ645538.1|     100.00  89      0       0       1       89      71502   71590   1e-41      165
HWI-ST1379:164:c5k28acxx:3:1101:2770:2209       gi|102567891|gb|DQ645538.1|     100.00  89      0       0       1       89      246653  246565  1e-41    165
HWI-ST1379:164:c5k28acxx:3:1101:2770:2209       gi|110287586|gb|DQ645537.1|     100.00  89      0       0       1       89      164556  164644  1e-41    165

 

ADD REPLYlink written 22 months ago by bpz30

Thanks a lot for your answers. I think BBsplit is the best tool for my problem. I will give it a try. 

ADD REPLYlink written 22 months ago by bpz30
1
gravatar for felipehcoutinho
22 months ago by
Brazil
felipehcoutinho10 wrote:

Assuming you have BLAST output files in the standard order, the identifier of the queries (names of illumina reads) that matched the sequences in your database should be in the first column. What I would do is write a script (e.g. using perl or python) to run through your BLAST table(s) and keep track of the query identifiers that match your mitogenomes, check if these queries have matches with a higher bitscore (last column of the BLAST output) to the the genomes you wanna screen out, and finally go through the file with all the illumina reads and filter only the ones you are interested in. You also should decide what you wanna do with the reads that match none of the genomes in the database. Hope this helps.

ADD COMMENTlink written 22 months ago by felipehcoutinho10
0
gravatar for h.mon
22 months ago by
h.mon6.6k
Brazil
h.mon6.6k wrote:

It seems BBSplit does exactly what you want, binning reads according to which reference they map.

If you intend to bin (possibly millions of) raw Illumina reads, Blast is not the best tool, it will be too slow.

ADD COMMENTlink written 22 months ago by h.mon6.6k
0
gravatar for Josh Herr
22 months ago by
Josh Herr5.4k
University of Nebraska
Josh Herr5.4k wrote:

This should be pretty straight forward as you should have your output in tabular format.  I do this quite frequently.

1. Sort on hits to your target genomes and output a list of the FASTA sequence headers.

2. Then I use a tool (the one I use is seqtk, but there are others) to input a list of these headers to subset the sequences out of your FASTA file into a new smaller FASTA file.

From there, you should be good -- let us know if you're still having problems selecting your BLAST hits. 

ADD COMMENTlink written 22 months ago by Josh Herr5.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 656 users visited in the last hour