Hi, I'm trying to get differential splicing information from some RNA reads using leafcutter. My annotation file is in gff3 format but leafcutter needs a gtf file. I tried converting it using gff read. I get this error message and don't really know what it means:
Error parsing target start coordinate from GFF line:
PGA_scaffold23__176_contigs__length_16134482 repeatmasker match 11978391 11978406 13 + . ID=PGA_scaffold23__176_contigs__length_16134482:hit:3923908:1.3.0.239;Name=species:GA-rich|genus:Low_complexity;Target=species:GA-rich|genus:Low_complexity -2 79 +
I hope someone can help me with this.
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written
by
LucasK •
1 answer
Apart from gffread,please try the following methods also for conversion. If it is still not working with any, then probably the gff file is not proper. Check the source and verify the correctness.
genome tools
http://genometools.org/tools/gt_gff3_to_gtf.html
ea-utils
https://github.com/ExpressionAnalysis/ea-utils/blob/master/clipper/gff2gtf
pasa
https://github.com/PASApipeline/PASApipeline/blob/master/misc_utilities/gff3_to_gtf_format.pl
kent utils:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
gff3ToGenePred followed by genePredToGtf
GFFtools-GX
https://github.com/vipints/GFFtools-GX/blob/master/gff_to_gtf.py
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