Hi All,
We have fastq files from a gut microbiome projects. I used 16S metagenomic kit from Ion torrent and sequenced them on Ion PGM, analyzed data on Ion Reporter and now I want to remove Prevotella Copri Sequence from the FASTQ file and reanalyze them. I'm just wondering whether anyone has done something like this. In Qiime, there is some information but I do not have Qiime output files such as otu_map.txt. http://qiime.org/scripts/filter_fasta.html My plan is to remove P. copri sequence from the FASTQ file and reanalyze them on Ion Reporter again.
Your inputs are much appreciated. Many thanks, Thilini
2 answers
I'm unfamiliar with Ion torrent data, but I guess this should work. You could try mapping all reads to the Prevotella Copri genome and then extract those which aren't mapped (and as such attributable to other species).
I think the method suggested by genomax wil be more efficient and less error prone for this application.
You can use bbsplit.sh from BBMap for this purpose. You will provide bbsplit will Prevotella copri sequence and it can bin the reads into two files. One for Prevotella and one for rest.
You need to run bbsplit.sh program from BBMap suite. You must have Provotella genome in a fasta file, if not you should be able to get that from NCBI easily. You would do something like
bbsplit.sh in=orig_reads.fq ref=provotella.fa basename=out_%.fq outu=clean_reads.fq
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