gffread error when converting gff to gtf

Question

[LucasK]

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.

Answer 1

[Jeffin Rockey]

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