Entering edit mode
4.7 years ago
Bioinfonext
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460
Hi,
I am getting error while running HTseq, could you please suggest what is the issue; I am using this command
$ htseq-count Oryza_indica.ASM465v1.44.chr.gff3 Leaf_T1_F_R10_S1_L001.sam >count.txt
$ htseq-count Oryza_indica.ASM465v1.44.chr.gff3 Leaf_T1_F_R10_S1_L001.sam >count.txt
Error occured when processing GFF file (line 1 of file Leaf_T1_F_R10_S1_L001.sam):
need more than 3 values to unpack
[Exception type: ValueError, raised in __init__.py:210]
Thanks Yogesh
Hi
I am still getting error:
Off file looks like this: I have downloaded it from ensemble :https://plants.ensembl.org/info/website/ftp/index.html but for genome indexing I used GTF file, should I convert the same gif to gif and then use it?
$ vi Oryza_indica.ASM465v1.44.chr.gff3
But When I am using GTF files, it is not showing error: so can I use GTF file instead of GFF3
Yes you can use
GTF
instead ofGFF3
, I would recommend using whichever file you used for alignment for the sake of consistency.Thanks a lot for your help Shawn!