Getting fastq files as the output of bowtie2
I am trying to use bowtie2 to filter out rRNs from my RNAseq data and as output I would like to get 2 fastq files:
- clean data (my RNAseq data without
rRNAs reads) rRNAs readsthat are removed from my RNAseq fastq file
All the commands that I found return sam or bam files. How can I get such fastq files using bowtie2?
2 answers
I am going to address what you are after rather than what you are asking (known as the XY Problem), read this post:
Cleaning RNA-Seq data from rRNA
the TLDR is:
You could use a tool like SortMeRna https://bioinfo.lifl.fr/RNA/sortmerna/
Or not do anything at all and carry on with the analysis,
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Istvan Albert
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Reach out to your core and ask them if they did ribodepletion step.