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Old 08-07-2021, 04:37 AM   #1
Junior Member
Location: Australia

Join Date: May 2012
Posts: 9
Default Hisat2 output is empty

I run this command:

hisat2 -p 40 -q -x Ene_index --sra-acc SRR13696274 --al alignedRNA_1 -S alignment1

and the output says:
4249510 reads; of these:
4249510 (100.00%) were unpaired; of these:
3194713 (75.18%) aligned 0 times
1045690 (24.61%) aligned exactly 1 time
9107 (0.21%) aligned >1 times
24.82% overall alignment rate

However, the produced alignedRNA_1 file is empty

Does anyone know what the problem may be?

Niloofar is offline   Reply With Quote
Old 08-14-2021, 07:48 PM   #2
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Location: Australia

Join Date: May 2012
Posts: 9

Ok - here's the reply I got from the developers, which solved the problem

Hi Niloofar,

Thank you for your reporting.
Could you download the SRA file (use fastq-dump program from SRAToolkit) and run HISAT2 with the file again?
There is a problem when you use --sra-acc and --al (--al*, --al-conc* , --un-conc* options) together, HISAT2 doesn't create read files properly. We'll fix it.

Niloofar is offline   Reply With Quote

--all, empty output, hisat2

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