I am comparing these alignment tools:
hisat2 (v2.0.4)
gsnap (v2016-08-24)
star (v2.5.2b)
tophat2 (v2.1.1)
by mapping a small set of RNAseq illumina samples vs. an annotated reference. And then I'm using samtools flagstat (samtools v0.1.18) to look at the % of reads that map. But the results I'm getting don't make sense.
For hisat2 & gsnap, flagstat is reporting the input read count (the top line of the output) as being more reads than are actually in the fastq files. Are the bamfiles generated by those aligners incompatible with flagstat?
For star & tophat2 its saying the total input read counts are equal to the # mapped in every case (i.e. 100% mapped for all samples), but I think thats simply because the output bams are only the 'hits'. So that makes sense to me. I just don't understand the hisat2 & flagstat results.
Can anyone explain what I'm seeing for hisat2 & gsnap? Is there an alternate tool I could use to report % reads mapped?
hisat2 (v2.0.4)
gsnap (v2016-08-24)
star (v2.5.2b)
tophat2 (v2.1.1)
by mapping a small set of RNAseq illumina samples vs. an annotated reference. And then I'm using samtools flagstat (samtools v0.1.18) to look at the % of reads that map. But the results I'm getting don't make sense.
For hisat2 & gsnap, flagstat is reporting the input read count (the top line of the output) as being more reads than are actually in the fastq files. Are the bamfiles generated by those aligners incompatible with flagstat?
For star & tophat2 its saying the total input read counts are equal to the # mapped in every case (i.e. 100% mapped for all samples), but I think thats simply because the output bams are only the 'hits'. So that makes sense to me. I just don't understand the hisat2 & flagstat results.
Can anyone explain what I'm seeing for hisat2 & gsnap? Is there an alternate tool I could use to report % reads mapped?
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