Dear CLIPcontext team,
I am working with a cytoplasmic RBP, and both CLIPcontext and peakhood would be very useful in working with exonic peaks.
When launching clipcontext G2T, in throws the following error
Traceback (most recent call last): File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/clipcontext/bin/clipcontext", line 2113, in <module> main_g2t(args) File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/clipcontext/bin/clipcontext", line 506, in main_g2t tr_seqs_dic = cliplib.get_transcript_sequences_from_gtf(args.in_gtf, args.in_2bit, File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/clipcontext/lib/python3.9/site-packages/clipcontext/cliplib.py", line 2810, in get_transcript_sequences_from_gtf gtf_extract_exon_bed(in_gtf, tmp_bed, tr_ids_dic=tr_ids_dic) File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/clipcontext/lib/python3.9/site-packages/clipcontext/cliplib.py", line 1902, in gtf_extract_exon_bed assert c_gtf_ex_feat, "no exon features read in from \"%s\"" %(in_gtf) AssertionError: no exon features read in from "Mus_musculus.GRCm38.102.gtf"
In the documentation, it is stated that clipcontext was designed and tested for hg38. Do you think this has something to do with using mm10?
Is there something that I could be doing wrong?
Thanks a lot.
Raul
Dear CLIPcontext team,
I am working with a cytoplasmic RBP, and both CLIPcontext and peakhood would be very useful in working with exonic peaks.
When launching clipcontext G2T, in throws the following error
Traceback (most recent call last): File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/clipcontext/bin/clipcontext", line 2113, in <module> main_g2t(args) File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/clipcontext/bin/clipcontext", line 506, in main_g2t tr_seqs_dic = cliplib.get_transcript_sequences_from_gtf(args.in_gtf, args.in_2bit, File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/clipcontext/lib/python3.9/site-packages/clipcontext/cliplib.py", line 2810, in get_transcript_sequences_from_gtf gtf_extract_exon_bed(in_gtf, tmp_bed, tr_ids_dic=tr_ids_dic) File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/clipcontext/lib/python3.9/site-packages/clipcontext/cliplib.py", line 1902, in gtf_extract_exon_bed assert c_gtf_ex_feat, "no exon features read in from \"%s\"" %(in_gtf) AssertionError: no exon features read in from "Mus_musculus.GRCm38.102.gtf"In the documentation, it is stated that clipcontext was designed and tested for hg38. Do you think this has something to do with using mm10?
Is there something that I could be doing wrong?
Thanks a lot.
Raul