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Filter 18s sequences using HMMs?
Hi all,
Apologies if this has been covered before but I'm fairly new to this and can't seem to find an answer to my question anywhere,
I've been using rRNAselector to filter out 16s fragments from my 250bp PE illumina shotgun reads with good success, however it is limited in that it can only filter out reads using the pre-packaged 16s HMM profiles that come with the program.
I'm now wondering if anyone knows of a similar tool which can use custom built HMM profiles to filter out reads from metagenomic libraries, as I'd like to try the same thing with 18s and possibly functional gene fragments. Is it as simple as building a profile with hmmbuild and using hmmalign to gt the reads which hit and filtering those out?
One thing I like about rRNAselector is that it trims all non-16s sequences from the reads which hit too (which makes it useful for downstream analysis in qiime) if anyone knows of a tool which can do this too I'd be eternally grateful!
any help at all would be great,
Many thanks,
Jonny
Apologies if this has been covered before but I'm fairly new to this and can't seem to find an answer to my question anywhere,
I've been using rRNAselector to filter out 16s fragments from my 250bp PE illumina shotgun reads with good success, however it is limited in that it can only filter out reads using the pre-packaged 16s HMM profiles that come with the program.
I'm now wondering if anyone knows of a similar tool which can use custom built HMM profiles to filter out reads from metagenomic libraries, as I'd like to try the same thing with 18s and possibly functional gene fragments. Is it as simple as building a profile with hmmbuild and using hmmalign to gt the reads which hit and filtering those out?
One thing I like about rRNAselector is that it trims all non-16s sequences from the reads which hit too (which makes it useful for downstream analysis in qiime) if anyone knows of a tool which can do this too I'd be eternally grateful!
any help at all would be great,
Many thanks,
Jonny