jaffal_epi2me-labs/wf-transcriptomes

[Cristoforo Grasso]

Dear all, 

I would like to use Jaffal, withinepi2me-labs/wf-transcriptomes pipeline. however it is not clear from the documentation, how could i use Jaffal within the epi2me-labs/wf-transcriptomes pipeline?

Could you please give me some help?

[Nadia Davidson]

Hi,

I would start by looking at the documentation from nanopore (e.g. https://labs.epi2me.io/workflows/wf-transcriptomes/) and go from there. We don't maintain the implementation of JAFFAL in epi2me, but I've got no doubt the nanopore software developers will be able to help you. Best of luck with you analysis.

Cheers,

Nadia.

[Miles Benton]

Hi @cristoforo

Sorry, I'm not 100% clear on what you are asking here. As Nadia mentioned, JAFFAL is included in the EPI2ME workflow "wf-transcriptomes', which she also kindly linked. If you want a specific example of how to include it in your analysis you can run the example on the provided test/demo code:

nextflow run epi2me-labs/wf-transcriptomes \

--fastq  differential_expression/differential_expression_fastq \
--de_analysis --ref_genome differential_expression/hg38_chr20.fa \
--transcriptome-source reference-guided \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap2_index_opts '-k 15'  --sample_sheet differential_expression/sample_sheet.csv \
--jaffal_refBase differential_expression/chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22 \
-profile standard

If you successfully run that then you can essentially substitute the data with your own, and then follow the documentation as to which files are recommended for reference/JAFFAL etc.

If you have any specific issues I would kindly ask you to raise them on the Github repository issues board, locate here: https://github.com/epi2me-labs/wf-transcriptomes/issues 

Cheers, 

  Miles