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Old 10-18-2016, 09:57 AM   #1
Ursus07
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Default HISAT2 unmapped reads

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?
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Old 10-21-2016, 05:27 AM   #2
bifosw
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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.
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Old 10-21-2016, 04:11 PM   #3
Ursus07
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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.
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