[BioC] DEXSeq output - count file

[Rao,Xiayu]

Hello,

DEXSeq is a great tool. Thank you for that. I recently generate my own gtf file with the same format as the exon.gff generated by dexseq_prepare_annotation.py. However, the output is strange. I tried to find the reason with no success. Could you please provide any idea about that problem? Thank you very much in advance!

Note: I used the latest dexseq, and the sam files had been sorted. 

1       genes.gtf       exonic_part     12228   12594   .       +       .       exonic_part_number "001"; gene_id "ENSG00000223972"
1       genes.gtf       exonic_part     12722   12974   .       +       .       exonic_part_number "002"; gene_id "ENSG00000223972"
1       genes.gtf       exonic_part     13053   13220   .       +       .       exonic_part_number "003"; gene_id "ENSG00000223972"
1       genes.gtf       exonic_part     14830   14969   .       -       .       exonic_part_number "001"; gene_id "ENSG00000223972+ENSG00000227232"
.............


==> SRR791043_counts.txt <==
:001G00027000003"
:002G00021000003"
:003G00070000003"
:004G00040000003"
:005G00060000003"
:006G00030000003"
:007G00019000003"
:008G00045600003"
:009G00020400003"
:001G00000000005"


Thanks,
Xiayu