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.