Problem when filtering splicing event with ENSEMBL GTF file.

Hi, I want to filter the splicing event by briekit-event-filter funciton. But some error and warnings came out. The GTF and fa files were downloaded from ENSEMBL. I assume that briekit may not support the chromosome name without 'chr'.

Could you give me some suggestions to fix it?

Here is my code to generate splicing GFF file and filter them:

Gfa=~/genome/ensembl/release97/mus_musculus/dna_seq/Mus_musculus.GRCm38.dna.primary_assembly.fa
GeGtf=~/genome/ensembl/release97/mus_musculus/dna_anno/Mus_musculus.GRCm38.97.gtf
briekit-event -a ${GeGtf} -o ./AS_events
for type in A3SS A5SS MXE RI SE
do
    # lenient filtering
    briekit-event-filter -a ./AS_events/${type}.gff3.gz --anno_ref=${GeGtf} -r ${Gfa} -o ./AS_events/${type}_lenient.gff3.gz \
                         --add_chrom X,Y --as_exon_min 10 --as_exon_max 100000000 --as_exon_tss 10 --as_exon_tts 10 --no_splice_site
done

Here are the total number of rows of splicing annotation GFF files:

$ for file in AS_events/*gz; do zcat $file | wc -l; done
41839
22365
11961
16332
104048

The Information returned can be checked in here.

huangyh09 / briekit

Problem when filtering splicing event with ENSEMBL GTF file. #3