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Old 09-21-2010, 01:51 AM   #1
Location: UK

Join Date: Jan 2010
Posts: 49
Default cufflinks version 0.8.2 vs 0.8.3

I ran 0.8.2 few months ago for a project and it worked fine on my .SAM files. After downloading 0.8.3, it started giving me a sort error.

I sorted my files exactly the same way as I did with 0.8.2. My .SAM file actually works with 0.8.2, but not 0.8.3. Is there something new with how it checks sorting in the new version? I noticed it was throwing me a sorting error based on reference contig name. Do I need to sort my .SAM file based on reference contig name and coordinates in the new version?
damiankao is offline   Reply With Quote
Old 09-21-2010, 10:08 AM   #2
Location: Stanford, CA

Join Date: May 2010
Posts: 88

If you use the sort command suggested by cufflinks

Something like this (it should be printed out when it gives the sorting error):
sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted

Then it will work

the (-k 3,3) indicates that the reference contig name must also be sorted.
SpliceMap: De novo detection of splice junctions from RNA-seq
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