threads

[zengyuan-11]

Can I speed up the processing of TEtranscripts by increasing the number of threads? If so, how can I do that?

[olivertam]

Hi,

If you wish to parallelize TEtranscripts, we would recommend running TEcount on each of your library to generate the count tables. You can then join them together and run DESeq2 afterwards to perform your differential analysis.

Thanks.

[zengyuan-11]

Thank you very much for your response.

But I'm still a bit confused about how to run TEtranscripts separately. How can I modify this to run each sample in parallel? Could you provide an example?My current command is:

nohup TEtranscripts --sortByPos --format BAM -t SRR14934120.bam SRR14934123.bam SRR14934127.bam SRR14934129.bam SRR14934131.bam -c SRR14934176.bam SRR14934189.bam SRR14934208.bam SRR14934210.bam SRR14934211.bam --GTF re_gene.gtf --TE TE2.gtf --mode multi --outdir out1 &

[olivertam]

Hi,

You can run TEcount as follows:

$ TEcount --sortByPos --format BAM -b [BAM file] --GTF re_gene.gtf --TE TE2.gtf --mode multi --outdir out1 --project [PREFIX]

Please note that each TECount run will use similar resources as the TEtranscripts run, so ensure that you have sufficient memory.

Thanks,

[zengyuan-11]

Thank you very much for your answer. I understand now.