Originally posted by DrS
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I just downloaded and installed the one from:
The file is:
HTSeq-0.5.4p3.tar.gz
The version still reports as:
Written by Simon Anders ([email protected]), European Molecular Biology
Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
Public License v3. Part of the 'HTSeq' framework, version 0.5.4p1.
.... And I still get the crash.
100000 GFF lines processed.
200000 GFF lines processed.
296737 GFF lines processed.
Warning: Malformed SAM line: MRNM != '*' although flag bit &0x0008 set
Warning: Malformed SAM line: RNAME != '*' although flag bit &0x0004 set
Segmentation fault
I'm thinking I'm going to have to try another aligner and see if that works
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It's actually an easy fix to get the most recent version running. If you open the htseq-count file in a text editor, you'll see that it mentions the exact version (you can have multiple versions installed). Assuming everything with the newest version is setup correctly, you can just change "p1" to "p3" and things should work. BTW, which aligner are you using? I've had good experience with tophat2 and, more recently, STAR.
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I was using Bowtie2 - paired-end genomic data from a 250x250 miSeq run.
I've asked others to chime in if they're also only having problems with paired-end data.
I'll try STAR next, but have meetings most of today so it might take a day or two to get to it.
And sorry about the mistaken identity
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GMAP and HTseq problems
I use GMAP to align my RNA-seq and then I use HT-Seq to get the counts. When i run the HTseq count script, it always complains of the sam file not being sorted.
I have used from picard tools, samtools and sort command to sort my SAM file but still it complains.
Picard tools (SortSAM)
SAmtools (convert from SAM to BAM, sort BAM file, Index BAM file, reconvert to BAM file).
Any reason? The HT-Seq count tools works well with tophat alignments
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