search

nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
https://nf-co.re/rnaseq
MIT License
896 stars 705 forks source link

FastQ Screen #905

Closed cutleraging closed 1 year ago

cutleraging commented 1 year ago

Description of feature

Hello,

Thanks for such an easy to use and information rich pipeline. An important part of my RNA-Seq pipelines is to quickly screen for any contamination. This is easily done using the FASTQ Screen program. Do you think this could be added?

https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

Ronnie

drpatelh commented 1 year ago

Hi @cutleraging. We have talked about this before but I don't think FastQ Screen is suitable for a pipeline like this because you would have to build loads of Bowtie2 indices for different genomes which is time intensive. Downloading them from S3 would be an option but again these will be quite large. You will pick up the common and expected source of contamination but it won't be comprehensive.

A number of other tools like Kraken2 have been developed to look for this sort of thing in a more unbiased way but in that case we would need to find the appropriate databases to use and could again face issues with size and download time. My preference would be for users to do this sort of thing independently of the pipeline like I have suggested in the issue below: https://github.com/nf-core/demultiplex/issues/36

Will close this for now but thanks for the feature request.