ribosomal RNA filtering

Question: ribosomal RNA filtering

2.0 years ago by

Carlos Andrés Caicedo • 0

Colombia/Medellín

Carlos Andrés Caicedo • 0 wrote:

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 COMMENT • link •

modified 2.0 years ago • written 2.0 years ago by Carlos Andrés Caicedo • 0

2.0 years ago by

Devon Ryan • 1.9k

Germany

Devon Ryan • 1.9k 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 COMMENT • link written 2.0 years ago by Devon Ryan • 1.9k

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

ADD REPLY • link written 2.0 years ago by Nicola Soranzo • 70

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

ADD REPLY • link written 2.0 years ago by Devon Ryan • 1.9k

2.0 years ago by

Carlos Andrés Caicedo • 0

Colombia/Medellín

Carlos Andrés Caicedo • 0 wrote:

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

Thank you very much.

ADD COMMENT • link written 2.0 years ago by Carlos Andrés Caicedo • 0

Please log in to add an answer.

Similar posts • Search »