backofenlab/clipcontext

Extract CLIP-seq binding regions with both genomic and transcript context

clipcontext's Issues

Add html report, showing sequence statistics for transcript and gene sequences

Optionally allow extraction of sequences in INT mode

Include center + extend to get sequences for intronic sites, or add one more mode with BED input and extension or optionally centering + extending.

Put CLIPcontext on bioconda / make conda package

Reduce library dependencies on Linux command line tools (for future versions)

Command line tools currently used by CLIPcontext:
cat, cut, diff, echo, grep, mv, sort, bedtools, twoBitInfo, twoBitToFa

Working with CLIPcontext in mm10 assembly

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