Question

dexseq_count.py SAM "NH" taq

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Jose M Garcia Manteiga ▴ 310

@jose-m-garcia-manteiga-6046

Last seen 7.7 years ago

Italy

> 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 [[alternative HTML version deleted]]

DEXSeq DEXSeq • 1.9k views

ADD COMMENT • link 10.8 years ago Jose M Garcia Manteiga ▴ 310

score 0 · Answer 1 · 2014-02-20

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 [[alternative HTML version deleted]]

score 0 · Answer 2 · 2014-02-20

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 at hsr.it > <mailto:garciamanteiga.josemanuel at="" hsr.it="">