Question: HISAT2 on multiple samples
gravatar for Sammy
6 weeks ago by
Sammy10 wrote:


I am using HISAT2 to align publicly available data. I have around 100 samples of paired-end reads.

hisat2 -p 8 -x refgenome --sra-acc SRRxxxxxxx,SRRxxxxxxx,SRRxxxxxxx

But I am not sure how to manage the output. I tried -S out1_file.bam out2_file.bam out3_file.bam but it doesn't seem to work. It looks like only one output can be specified. What is there that I am missing? I don't really want to run one sample at a time.

Equally I can use SRAToolkit to upload the samples and then feed the fasta files to hisat2 (-1 reads1 -2 reads2) instead of ---sra-acc. However, it looks way more tedious and I am pretty sure I am going to have the same problem with the output as I want to run multiple samples at once.

I hope I was clear enough.


rna-seq • 68 views
ADD COMMENTlink modified 6 weeks ago by swbarnes27.5k • written 6 weeks ago by Sammy10
gravatar for swbarnes2
6 weeks ago by
United States
swbarnes27.5k wrote:

You can't get HISAT to take in 100 input file pairs and give you 100 output files.

What you can do is make a loop that will go through each pair one after the other. Or get different commands of HISAT working at the same time.

ADD COMMENTlink written 6 weeks ago by swbarnes27.5k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1235 users visited in the last hour