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PalMuc / TransPi

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
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Can I inform the direction of sequencing? #57

Open katiacapel opened 1 year ago

katiacapel commented 1 year ago

Hi,

How does the pipeline deals with the direction of sequencing, is there a way to inform it (for example, if it is stranded)? If there is a way to include this information, how can I do that?

Thank you! Kátia

sevragorgia commented 1 year ago

Hi Kátia,

I don't think this is possible. The Trinity cmd line used by TransPi looks as follows:

Trinity --max_memory \${mem}G --seqType fq --left ${left} --right ${right} --CPU ${task.cpus} --no_normalize_reads --full_cleanup --output trinity_out_dir

You can see is not assigning any strandedness. I cannot find any option to do it on the command line.

If you want to use the stranded option in Trinity (or other assemblers) you can modify the TransPi.nf process function to use the corresponding option. You can do that in your local TransPi.nf nextflow file.

Is not very elegant but is an option. Please report back if you decide to do this and if it works and note that if you plan to assemble multiple transcriptomes in one go, ALL will have to be stranded. I think this is the reason the strandedness is not used: you cannot turn the option on and off for independent datasets if you want to assemble more that one transcriptome at a time, which is possible in TransPi.

hope it helps,

Sergio