I will take this chance to mention that the python scripts from dexseq from the most recent versions accept also files ordered by position, rather than only sorted by read name as well as bam files. You can specify this in the parameters '-f' and '-r'. The bam file reader will require also a recent version of HTSeq (0.5.4p4). The option of reading files sorted by position will require a bit more RAM, however I was able to run it for a bam file containing reads from a full lane in my 8 Gb RAM laptop. Hope it is useful! Alejandro > Hi Margaret, > > It's expecting a SAM file, not a BAM file: > > samtools view -h ahBC010.sam.bam | dexseq_count.py -p yes -s no hs71.gff - ahBC010.counts > > Note that - specifies reading from the standard input rather than a file. > > Cheers, > Devon > > ____________________________________________ > Devon Ryan, Ph.D. > Email: dpryan at dpryan.com > Tel: +49 (0)178 298-6067 > Molecular and Cellular Cognition Lab > German Centre for Neurodegenerative Diseases (DZNE) > Ludwig-Erhard-Allee 2 > 53175 Bonn, Germany > > On Oct 6, 2013, at 9:41 PM, Margaret Linan wrote: > >> Hi Simon, >> >> The sort code worked just fine. I also ran a diagnostic on the *.bam files >> and no error came up. But when I tried to use the sorted >> *.sam.bam file with the dexseq_count.py program, I got the following >> messages: >> >> >> [mlinan at s59-14 MISC]$ python dexseq_count.py -p yes -s no hs71.gff >> ahBC010.sam.b am BC010.counts >> Traceback (most recent call last): >> File "dexseq_count.py", line 132, in <module> >> for af, ar in HTSeq.pair_SAM_alignments( HTSeq.SAM_Reader( sam_file ) ): >> File >> "/packages/python/python-2.7.3/lib/python2.7/site- packages/HTSeq/__init__ >> .py", line 610, in pair_SAM_alignments >> for almnt in alignments: >> File >> "/packages/python/python-2.7.3/lib/python2.7/site- packages/HTSeq/__init__ >> .py", line 549, in __iter__ >> algnt = SAM_Alignment.from_SAM_line( line ) >> File "_HTSeq.pyx", line 1274, in HTSeq._HTSeq.SAM_Alignment.from_SAM_line >> (src /_HTSeq.c:22184) >> ValueError: ('SAM line does not contain at least 11 tab-delimited fields.', >> 'lin e 1 of file ahBC010.sam.bam') >> >> When I opened the *sam.bam file I found the below in the first few lines. >> The entire file is a collection of random symbols with accents marks and >> numbers. >> >> >> ????????BC???"?kA????\"T >> >> "W?????????].????A?????????vsI!?? h)6v??M?.?"???] ?8;"?Y >> >> ????g??}^fg??NJ?????+5\E????v? >> >> ?(?35Y_?[^????q%a?#? (??2F]???S????W`b1 >> >> >> ? >> >> L >> >> ??)v >> >> F???????b?(?????D"?????? >> >> >> >> Thanks, >> >> Margaret >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >