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Hi everyone,
I have some problems with a recent mapping I did with STAR. I run the following command:
In the resulting sam file I find quite a lot of entries looking like this:
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.
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
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
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.
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