Error with HTSeq

Running HTSeq to get raw read counts associated with chromosomal positions/annotated genes from sorted .bam files:

Error occurred when processing SAM input (record #30675291 in file {PATH}/tophat/Exp-1-Basal/accepted_hits.sorted.bam):
 Maximum alignment buffer size exceeded while pairing SAM alignments.
 [Exception type: ValueError, raised in __init__.py:671]

Simon Anders, the author of the package from EMBL Heidelberg, suggested in this forum post to remove the “-r pos” or “–order=pos” argument. I did this and it seems to work fine now. Interesting that I had run HTSeq before with a different data set of sorted bam files and did not get this error.

HTSeq manual page: http://www-huber.embl.de/users/anders/HTSeq/doc/count.html

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About Lisa Johnson

PhD candidate at UC Davis.
This entry was posted in Bioinformatics, software. Bookmark the permalink.

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