Transcripts to consider for analysis

There seems to be an inconsistency between the gtf file and the cDNA file from ENSEMBL. See here

• Which transcripts should we use for the pipeline
• Add scripts or/and rules to select the transcripts

changed the description

At this point I wouldn't worry about this and leave it for the user to decide. We can of course discuss this for internal use...

added Discuss label

added To Do label

removed To Do label

changed milestone to %v0.1.0 release

Oh, I misread the issue. Thought it was about filtering transcripts/annotations. As far as I know Ensembl splits up their transcript FASTA files into separate files, cDNA and non-coding. But I think even then there may be inconsistencies with the gene annotations file. Using scripts to keep the files consistent is tedious. The easiest and sanest solution here should be to use the gene annotation file as a single source of truth and derive the transcriptome from that with the help of the genome. And it has the additional advantage that we require one input file less for the workflow.

As there is already an issue for this (#62 (closed)), I will close this one.

closed

assigned to @kanitz