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Old 10-07-2010, 10:33 AM   #5
Pejman
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Location: Switzerland

Join Date: Jul 2010
Posts: 23
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Quote:
Originally Posted by tguo View Post
Hi all,


Everything seems to work fine if I don't use a reference GTF.
I have the same problem. I'm using cufflinks-0.9.1.Linux_x86_64 and trying to get it to produce expression levels based on a GTF file. If I run it without a reference GTF file, it works fine, gives some expressions. But with reference:
Code:
$cufflinks -G hg18_annotation.gtf MyFile.sam
it gives:
Code:
[20:24:17] Inspecting reads and determining fragment length distribution.
> Processing Locus chr6:27032750-27099732      [*****************        ]  69%
Error: this SAM file doesn't appear to be correctly sorted!
        current hit is at chr10:272501, last one was at chr9:139953334
Cufflinks requires that if your file has SQ records in
the SAM header that they appear in the same order as the chromosomes names 
in the alignments.
If there are no SQ records in the header, or if the header is missing,
the alignments must be sorted lexicographically by chromsome
name and by position.

The GTF file I downloaded from UCSC genomebrowser portal and .sam file is produced by Bowtie, and then sorted by Samtools. Does anybody have any clue?
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