Open HenriettaHolze opened 1 week ago
Never mind, I clearly just can't read.
The known transcript IDs are given in the features.tsv.gz
file, I only need to match them to the genes.
Different question now though, all features in transcript_raw_feature_bc_matrix/features.tsv.gz
and transcript_processed_feature_bc_matrix/features.tsv.gz
have a ENST... ID but transcriptome.gff.gz
contains transcripts without the cmp_ref
flag. Are the novel transcripts not quantified per cell?
Cheers
Ask away!
Hi, I would look at transcript usage but all transcripts are "unknown". The file
transcript_processed_feature_bc_matrix/features.tsv.gz
contains only "unknown" transcripts.The
transcriptome.gff.gz
looks as follows:The pipeline takes a gtf file with transcript information as input.
Does this output mean that no transcripts given in the gff file were recovered, or does the pipeline not match transcripts identified by stringtie to known transcripts? Or is there an option to not run stringtie but only quantify known transcripts given in the gtf file?
Cheers,
Henrietta