Why didn't this tool remove the genomic information of the host, such as human or mouse?

[luozhy88]

1 Why didn't this tool remove the genomic information of the host, such as human or mouse? 2 Why didn't this tool remove common contaminant ?

[fpusan]

1) Because you didn't ask it to. See the manual of v1.6 (option --filter in sqm_mapper.pl) to see how it's done. 2) You can preprocess your reads with sqm_mapper.pl to remove host reads and whatever else you think would be a "common contaminant". We don't do this by default, since the definition of "common contaminant" is context and researcher-dependent.

[fpusan]

You need to define what you want to consider "common contaminants" in the scope of your study, and prepare the files for those yourself. We can not help with that.

[luozhy88]

How can use sqm_annot.pl? can you give an example?

[jtamames]

Please read the manual. All your questions can find a solution there.

[luozhy88]

I need to host 2 samples by sqm_mapper.pl, but the output is always a filtered sample for fq. Why?

[jtamames]

Could you please include the syslog file?

[jtamames]

Anyway, I think I got it. Change line 267, reading: if($filter) { filter($thissample,$outsam,$outdir,$pairs{$thissample}{pair1},$pairs{$thissample}{pair2}); exit; } by: if($filter) { filter($thissample,$outsam,$outdir,$pairs{$thissample}{pair1},$pairs{$thissample}{pair2}); next; } And run the script again

[luozhy88]

Thanks,it works!