Ok, I think for me it would be easier to just use the old version of the
count.py script.
Thanks for the prompt reply!
Jose


2014-02-20 13:30 GMT+01:00 Alejandro Reyes <alejandro.reyes@embl.de>:

> Hi Jose,
>
> Both of the solutions that you mention should work.  We need to think of
> a smarter solution for this, but it is difficult when the sam
> specifications can have many interpretations from the aligner authors!
>
> Best regards,
> Alejandro
>
>
> >
> >     Hi Alejandro,
> >     I have updated my dexseq_count.py and dexseq_prepare_annotation.py
> >     script to use it with the -r parameter to ignore the exons with
> >     overlap between genes. Now I am using dexseq_count.py like this:
> >
> >     dexseq_count.py -p yes -s no -a 10 -f sam -r name $SAM $GFF
> >
> >     *Traceback (most recent call last):*
> >
> >     *  File "/home/jgarcia/dexseq_count.py", line 225, in <module>*
> >
> >     *    rs = map_read_pair( af, ar )*
> >
> >     *  File "/home/jgarcia/dexseq_count.py", line 132, in map_read_pair*
> >
> >     *    if ar != None and ar.optional_field("NH") > 1:*
> >
> >     *  File "_HTSeq.pyx", line 1371, in
> >     HTSeq._HTSeq.SAM_Alignment.optional_field (src/_HTSeq.c:25899)*
> >
> >     *KeyError: 'SAM optional field tag NH not found'*
> >
> >
> >     My SAM files do not have indeed the NH tag, but with previous
> >     versions of the script it worked. The aligment is made by
> >     SOAPSplice that already gives you only single hits in our
> >     settings. I know ht-seq_count.py checks as well for the NH tag,
> >     but it does not yield an error and simply produces a 0 in
> >     multiple-alignments filed at the tail of the count file.
> >
> >     Do I have to add manually a NH tag =1 or can I use an older
> >     version of the dexseq_count.py script to skip this error? I have
> >     updated mainly to use the -r option in dexseq_prepare but I do not
> >     need using the -r or -f parameters
> >
> >     My version of DEXSeq is 1.8.0 and I had an older version under
> >     1.3.3 that worked
> >
> >     Thanks
> >
> >     Jose
> >
> >
> >
> >
> >
> >
> > --
> > Jose M. Garcia Manteiga PhD
> > Research Assistant - Data Analysis in Functional Genomics
> > Center for Translational Genomics and BioInformatics
> > Dibit2-Basilica, 3A3
> > San Raffaele Scientific Institute
> > Via Olgettina 58, 20132 Milano (MI), Italy
> >
> > Tel: +39-02-2643-4751
> > e-mail: garciamanteiga.josemanuel@hsr.it
> > <mailto:garciamanteiga.josemanuel@hsr.it>
>
>


-- 
Jose M. Garcia Manteiga PhD
Research Assistant - Data Analysis in Functional Genomics
Center for Translational Genomics and BioInformatics
Dibit2-Basilica, 3A3
San Raffaele Scientific Institute
Via Olgettina 58, 20132 Milano (MI), Italy

Tel: +39-02-2643-4751
e-mail: garciamanteiga.josemanuel@hsr.it

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