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@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.


‹�����ÿ�BC�ò¥"½kAÆÇœÆ\"T

"WØîÍ×ÎÎÌ™À].’ø‘AŽÍíÜÞÆÜîåvsI!‚ h)6vÖ‚MÁ.¶"ˆþ‚] …8;"ìY

·÷ð›gß÷}^fgËçNJ�ÔæÊë+5\EåÕÛµv’

‚(ö35Y_½[^Õå¥•q%aÈ#¸ (Ç˜2F]îòãSŒÇ°W`b1


É

L

ÆÚ)v

Fœº’¹¨ÀÌbÂ(¦’ØË±D"¹œÑ‚òœ



Thanks,

Margaret

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