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Missing transcriptome level differential expression analysis in the latest version #85

Open alyazeeditalal opened 2 months ago

alyazeeditalal commented 2 months ago 
          Dear @sarahjeeeze,

Would you please guide me in finding the results_dexseq.tsv containing the differential expression at the transcript level? This tsv file was produced using previous versions but I struggled to find it using the latest version.

Kind regards, Talal

Originally posted by @alyazeeditalal in https://github.com/epi2me-labs/wf-transcriptomes/issues/81#issuecomment-2049953812

sarahjeeeze commented 2 months ago

Hi, thanks for the feedback, I apologize. We have accidentally removed this from the output de_analysis folder, we will ensure it is output in the next release. In the meantime you should be able to find the file in the work directory of either the de_analysis process or make report process.

alyazeeditalal commented 2 months ago

Hi Sarah,

Thank you for your response and your consistent update on the pipeline.

Would you please also include the salmon count files among the output for both transcript and genes? this would be useful in case one would like to use these count files for other analyses using different R packages than the ones used in the pipeline.

The addition of the bam files with the output files has been useful to analyse the alignment files such as estimating the length of the reads aligning to a particular gene region.

Best wishes, Talal

sarahjeeeze commented 1 month ago

Sure we will consider and look in to this, in the meantime you should be able to find the count files in the de_analysis process work folder.