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  • 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:

    Code:
    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:

    Code:
    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.

  • #2
    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.

    Cheers
    Alex

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