Alaina Shumate
Alaina Shumate
I also experience the issue of simulatory.py hanging and not actually simulating any reads. Here is my command and parameters ref_g GRCh38.fa ref_t hg38c_protein_and_lncRNA_sorted.fa exp hg38_stranded_spacer.tpm model_prefix training out simulated_dRNA...
my issue was this line ` if transcript_id.startswith("ENS") and tpm > 0:` my transcripts in my expression file do not start with ENS so the dictionary of expression values was...
@SaberHQ we're using the RefSeq annotation which does not use ENS as prefixes to transcript ids. As far as i know that is specific to ensembl annotations. i deleted that...
can you please send the command you are using?
was the _db file properly created. if so what is its name?
can you try deleting that file and re-running liftoff?
Hi, can you please let me know which version of liftoff you are using? Thanks!
has a database of the gff been created in your working directory? it should be the same name as the annotation file with "_db" at the end. if so, can...
Hi I am not sure i understand your question. Are you saying that liftoff transferred more or less genes/features that what you expected from buso?
I am still having a bit of a hard time understanding what part of your results were unexpected. If i am reading this correct it seems like it was expected...