Getting fastq files as the output of bowtie2

Question

[Sara]

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:

1. clean data (my RNAseq data without rRNAs reads)
2. rRNAs reads that 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?

[cpad0112]

Reach out to your core and ask them if they did ribodepletion step.

Answer 1

[Istvan Albert]

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,

Answer 2

[cpad0112]

bam2fastq/sam2fastq may help you.