HISAT2 unmapped reads

[Ursus07]

Thanks for the reply! I was hoping there was a means of writing out only those mates that did not map anywhere rather than all reads that did not map concordantly, but it is a good place to start I suppose.

[bifosw]

Hi I had the same problem, you need to use --un-conc for paired end reads (write paired-end reads that fail to align concordantly to file(s) at <path>). There is an explanation of the relevant SAM flags in the help manual for Hisat2.

[Ursus07]

Hi all, I am using HISAT2 and trying to write unmapped reads from paired-end data and the flag --un is resulting in empty files. I know they are not all mapping so does anyone have any recommendations to write those reads to a file?