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Old 07-09-2014, 06:18 AM   #1
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Location: Germany

Join Date: Apr 2012
Posts: 215
Default Need help with STAR output (cigar string in sam file)

Hi everyone,

I have some problems with a recent mapping I did with STAR. I run the following command:

STAR --runMode alignReads --runThreadN 16 --genomeDir /path/to/genome --readFilesIn SE_454_reads.fastq --outFileNamePrefix outFileBla --outSAMstrandField cufflinks-like --outSAMattributes Standard
In the resulting sam file I find quite a lot of entries looking like this:

IQ4WJ2H01BD6DC	0	chr9	2261381	3	299M1I83M	*	0	0	NH:i:2	HI:i:1	AS:i:374	nM:i:1
IQ4WJ2H01BD6DC	256	chr9	2261381	3	300M1I82M	*	0	0	NH:i:2	HI:i:2	AS:i:374	nM:i:1
Why do I get this 1bp shift of the insertion (as indicated in the cigar) ?
Both alignments have obviously the same score but to output both is nonsense in my opinion.
Is anyone aware of a parameter with which I will get rid of the "duplicate".
I want to keep true multi-reads, so I cannot use "outFilterMultiMapNmax" and others of that kind.
WhatsOEver is offline   Reply With Quote
Old 07-09-2014, 07:37 AM   #2
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Location: NY

Join Date: Feb 2009
Posts: 161

Which version of STAR are you using?
Earlier versions had this problem - it's been fixed in the later releases.
Please try the latest patch.
If it does not help, please send me the read sequence and link to a genome you are mapping agains.

alexdobin is offline   Reply With Quote

sam cigar, star aligner

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