Closed eboileau closed 1 year ago
Added get-gtf-from-predictions
, but still needs to be tested on the TEA downstream. Option --gtf
added to run-htseq-workflow
. We need to add explanations in the docs regarding the usage of GTF with htseq-count --type X
, in particular if de_novo_gtf
is present.
Currently,
run-htseq-workflow
uses the GTF from the config (or the newly created GTF ifde_novo_gtf
is present), buttype=CDS
is used for counting. It is possible to override defaults e.g. using--type exon
, but somehow this didn't work as expected (possibly due to concatgtf
andde_novo_gtf
? Many entries are expected to overlap or even to be duplicated).But we could create our own GTF using the predictions, and run HTSeq-count on this, which would really give us count tables for the ORFs.