Hello!
I have an issue converting gff3>gtf using the
gffread utility in the
cufflinks package, in sense that I have an empty output file, no log.
Here is the detail of how I proceeded:
- generated the gff file by aligning the transcripts to the reference, using GMAP with option -f gff3_match_cdna to specify the output format
- convert gff3 to gtf using: gffread file.gff3 -T -o file.gtf
Here is an overview of the output format (
head) :
$ head r9_gmap_match-cdna.gff
##gff-version 3
# Generated by GMAP version 2017-04-24 using call: /home/aechchik/software/gmap-2017-04-24/bin/gmap.sse42 -d gmapidx -D /scratch/beegfs/monthly/aechchik/isoforms/ref/chromosomes/ -f gff3_match_cdna -n 0 -t 20 r9_2d.fasta
2L gmapidx cDNA_match 18442664 18443024 79 - .ID=ae6a7818-85b5-4739-8031-e58f4462ad41_Basecall_2D_2d.path1;Name=ae6a7818-85b5-4739-8031-e58f4462ad41_Basecall_2D_2d;Target=ae6a7818-85b5-4739-8031-e58f4462ad41_Basecall_2D_2d 141 489;Gap=M13 I10 M8 D3 M8 D3 M32 D1 M4 D2 M5 D3 M34 I3 M6 D1 M7 D1 M5 D1 M30 D2 M16 I1 M8 D3 M10 D1 M5 D1 M6 I1 M8 I1 M8 D1 M33 D3 M33 I1 M28 D3 M25
###
3R gmapidx cDNA_match 15853880 15855465 96 + .ID=dd2444cf-34d6-4cd3-87ab-0ae1f3cb1f96_Basecall_2D_2d.path1;Name=dd2444cf-34d6-4cd3-87ab-0ae1f3cb1f96_Basecall_2D_2d;Target=dd2444cf-34d6-4cd3-87ab-0ae1f3cb1f96_Basecall_2D_2d 80 1645;Gap=M46 D2 M12 D2 M157 D3 M4 D1 M50 I2 M3 I1 M12 I1 M68 I1 M66 I1 M53 D2 M47 D1 M16 D1 M35 D1 M155 D1 M28 D1 M166 D2 M47 D1 M8 D4 M69 D1 M28 D1 M5 D1 M12 D1 M202 I1 M115 D1 M61 I2 M7 D1 M7 I1 M36 D2 M41
3R gmapidx cDNA_match 15855529 15855742 97 + .ID=dd2444cf-34d6-4cd3-87ab-0ae1f3cb1f96_Basecall_2D_2d.path1;Name=dd2444cf-34d6-4cd3-87ab-0ae1f3cb1f96_Basecall_2D_2d;Target=dd2444cf-34d6-4cd3-87ab-0ae1f3cb1f96_Basecall_2D_2d 1646 1856;Gap=M21 D1 M68 D1 M85 D1 M37
###
X gmapidx cDNA_match 14837810 14838142 93 - .ID=960b50cd-945e-4c12-b9bc-367f965575bb_Basecall_2D_2d.path1;Name=960b50cd-945e-4c12-b9bc-367f965575bb_Basecall_2D_2d;Target=960b50cd-945e-4c12-b9bc-367f965575bb_Basecall_2D_2d 74 406;Gap=M13 D1 M182 I1 M14 I2 M56 I1 M30 D2 M21 D1 M13
X gmapidx cDNA_match 14837470 14837753 92 - .ID=960b50cd-945e-4c12-b9bc-367f965575bb_Basecall_2D_2d.path1;Name=960b50cd-945e-4c12-b9bc-367f965575bb_Basecall_2D_2d;Target=960b50cd-945e-4c12-b9bc-367f965575bb_Basecall_2D_2d 407 688;Gap=I2 M5 I1 M64 I1 M44 D1 M9 D5 M31 D3 M23 I1 M19 I1 M25 I1 M26 D1 M19 I1 M9
###
So actually the command results in an empty gtf file :(
Any ideas on how I fix this? I need gtf file to feed it in the
cuffmerge pipeline
I can of course provide the full file if necessary.
Thanks for your time.
Cheers,
Amina