Hello experienced colleagues,
I'm trying to filter out ribosome-related reads from my Illumina (Casava 1.8) pair-read (100 bp) data. The data was pre-filtered with Trimmomatic (adapters and low quality reads were removed). Now all this stuff exists in 3 files: “left.fq”, “right.fq” and “unpaired.fq”. Ribosome sequences are stored in the bowtie2-build “rRNA” base.
The simplest story about Bowtie2 syntax is in case of unpaired reads:
It works.
But, more dramatic situation arises if I want to get filtered pair-reads in 2 separate files and additionally reads from broken during filtration pairs in a 3-d file.
I'm trying to do the following:
But, bowtie2 outputs just concordant pairs in 2 files... broken pairs are lost.
How to get them?
I'm trying to filter out ribosome-related reads from my Illumina (Casava 1.8) pair-read (100 bp) data. The data was pre-filtered with Trimmomatic (adapters and low quality reads were removed). Now all this stuff exists in 3 files: “left.fq”, “right.fq” and “unpaired.fq”. Ribosome sequences are stored in the bowtie2-build “rRNA” base.
The simplest story about Bowtie2 syntax is in case of unpaired reads:
bowtie2 -p 8 --un /output/filt_unpaired.fq rRNA /input/unpaired.fq
But, more dramatic situation arises if I want to get filtered pair-reads in 2 separate files and additionally reads from broken during filtration pairs in a 3-d file.
I'm trying to do the following:
bowtie2 -p 8 -X 430 --un-conc /output/filt_pairs.fq rRNA -1 /input/left.fq -2 /input/right.fq
How to get them?
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