Hi,
Just finished installing HTSeq on a MacOSX with python 2.6.6 and latest version of Numpy.
I can execute the first few commands of the HTSeq tour using the yeast example sequence file so the install seems to be working
I invoked the htseq-counts script using the following:
>python -m HTSeq.scripts.count 45minCt_1.sam cneoh99.gtf
and I get the following error:
Error occured in line 1 of file cneoh99.gtf.
Error: The attribute string seems to contain mismatched quotes.
[Exception type: ValueError, raised in __init__.py:167]
The first few lines of my gtf file looks like:
Chr1 CNA2_FINAL_CALLGENES_1 start_codon 11499 11501 . - 0 "gene_id ""CNAG_00001""; transcript_id ""CNAG_00001T0"";"
Chr1 CNA2_FINAL_CALLGENES_1 stop_codon 11060 11062 . - 0 "gene_id ""CNAG_00001""; transcript_id ""CNAG_00001T0"";"
Chr1 CNA2_FINAL_CALLGENES_1 exon 11430 11501 . - . "gene_id ""CNAG_00001""; transcript_id ""CNAG_00001T0"";"
I've attached an excerpt of the file.
Do I need headers in this file?
Thanks for any help.
Regards,
Maureen
Just finished installing HTSeq on a MacOSX with python 2.6.6 and latest version of Numpy.
I can execute the first few commands of the HTSeq tour using the yeast example sequence file so the install seems to be working
I invoked the htseq-counts script using the following:
>python -m HTSeq.scripts.count 45minCt_1.sam cneoh99.gtf
and I get the following error:
Error occured in line 1 of file cneoh99.gtf.
Error: The attribute string seems to contain mismatched quotes.
[Exception type: ValueError, raised in __init__.py:167]
The first few lines of my gtf file looks like:
Chr1 CNA2_FINAL_CALLGENES_1 start_codon 11499 11501 . - 0 "gene_id ""CNAG_00001""; transcript_id ""CNAG_00001T0"";"
Chr1 CNA2_FINAL_CALLGENES_1 stop_codon 11060 11062 . - 0 "gene_id ""CNAG_00001""; transcript_id ""CNAG_00001T0"";"
Chr1 CNA2_FINAL_CALLGENES_1 exon 11430 11501 . - . "gene_id ""CNAG_00001""; transcript_id ""CNAG_00001T0"";"
I've attached an excerpt of the file.
Do I need headers in this file?
Thanks for any help.
Regards,
Maureen
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