Hi,
I am using DEXSeq package and I encountered some problem. First I used this comand "python dexseq_prepare_annotation.py -r no GRCh38.79.gtf GRCh38.79_DEXSeq.gff". the gff file looks below:
head GRCh38.79_DEXSeq.gtf
1 dexseq_prepare_annotation.py aggregate_gene 11869 14409 . + . gene_id "ENSG00000223972"
1 dexseq_prepare_annotation.py exonic_part 11869 12009 . + . transcripts "ENST00000456328"; exonic_part_number "001"; gene_id "ENSG00000223972"
1 dexseq_prepare_annotation.py exonic_part 12010 12057 . + . transcripts "ENST00000456328+ENST00000450305"; exonic_part_number "002"; gene_id "ENSG00000223972"
1 dexseq_prepare_annotation.py exonic_part 12058 12178 . + . transcripts "ENST00000456328"; exonic_part_number "003"; gene_id "ENSG00000223972"
1 dexseq_prepare_annotation.py exonic_part 12179 12227 . + . transcripts "ENST00000456328+ENST00000450305"; exonic_part_number "004"; gene_id "ENSG00000223972"
then I used
/script_human/pythonScripts/dexseq_count.py -p yes -f bam Aligned.noS.bam -r pos -s reverse GRCh38.79_DEXSeq.gff dexseq.txt
it gave me follwoing error
Traceback (most recent call last):
File "/script_human/pythonScripts/dexseq_count.py", line 94, in <module>
for f in HTSeq.GFF_Reader( gff_file ):
File "/home/asingh/.local/lib/python2.7/site-packages/HTSeq-0.6.1p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py", line 207, in __iter__
strand, frame, attributeStr ) = line.split( "\t", 8 )
ValueError: need more than 1 value to unpack
I also tried below script was posted some days ago to check gff file and it did not give any error, but when i run dexseq_count.py it shows error. At the moment I am using HTSeq-0.6.1p1 version.
import HTSeq
gff_file="GRCh38.79_DEXSeq.gff"
features = HTSeq.GenomicArrayOfSets( "auto", stranded=True )
for f in HTSeq.GFF_Reader( gff_file ):
if f.type == "exonic_part":
f.name = f.attr['gene_id'] + ":" + f.attr['exonic_part_number']
features[f.iv] += f
I generated bam file from star with sorted by position. Kindly give some suggestion.
Thanks!
As
