why hisat2 mapping sam file has many sam flags

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3.0 years ago

szp770 ▴ 10

Hi, I used hisat2 to map my reads to hg19 genome, and it seems there's something wrong with this sam file. The @PG header shows this:

@PG     ID:hisat2       PN:hisat2       VN:     CL:"envs/rna/bin/hisat2-align-s --wrapper basic-0 -p 8 --dta -x GRCh37.p13.genome.clean.fa -S 1.sam -1 1.non_rRNA_paired.fq -2 2.non_rRNA_paired.fq"

and the samtools flag in this sam file has many different numbers: 113 ,129,133,137,145 ,147,153,161,163,177,321,329,337,339,345,353,355,369,385,393,401,403,409,417,419,433,65,69,73,81,83,89,97,99. But usually the double-end sequencing files only has 99,147 or something else, but not so many samtools flag numbers, so what's wrong here?

sam RNA-seq sequencing hisat2 genome • 658 views

ADD COMMENT • link updated 3.0 years ago by GenoMax 141k • written 3.0 years ago by szp770 ▴ 10

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You can see explanation for those SAM flags using:
https://www.samformat.info/sam-format-flag
https://broadinstitute.github.io/picard/explain-flags.html

ADD REPLY • link 3.0 years ago by GenoMax 141k

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