[BioC] DEXSeq output - count file

[Alejandro Reyes]

Dear Xiayu Rao,

Thanks for your interest in DEXSeq.
That looks strange, does it happen when you use files different from the 
one you generated by your own? Could you maybe send me (offline) your 
gtf file and the first 1000 lines of one of your sam files?

Bests,
Alejandro

> 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