Question: ribosomal RNA filtering
0
gravatar for Carlos Andrés Caicedo
2.0 years ago by
Colombia/Medellín

There exist some tool available at Galaxy to remove rRNA? The RNAseq data were generated using an Illumina Hiseq2500

Thanks

Carlos

rna-seq galaxy • 718 views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Carlos Andrés Caicedo0
1
gravatar for Devon Ryan
2.0 years ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

Have a look at RiboGalaxy, which has a "remove rRNA using bowtie" tool. Note that in some cases (e.g., ribosomal profiling), you may find it useful to remove snoRNAs and other small non-coding RNAs as well (and probably tRNAs too).

This reminds me that maybe the bowtie2 or hisat2 wrappers should get updated to allow output of the unaligned reads in fastq format. That'd make this easier to do and not require a dedicated tool.

ADD COMMENTlink written 2.0 years ago by Devon Ryan1.9k
1

The devteam's Bowtie2 Galaxy wrapper already has the --un/--un-conc options implemented.

ADD REPLYlink written 2.0 years ago by Nicola Soranzo70

Thanks, I didn't see that when I looked. That'd be a good route for OP to take then.

ADD REPLYlink written 2.0 years ago by Devon Ryan1.9k
0
gravatar for Carlos Andrés Caicedo
2.0 years ago by
Colombia/Medellín

I did not know RiboGalaxy. I am going to try it.

Thank you very much.

ADD COMMENTlink written 2.0 years ago by Carlos Andrés Caicedo0
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