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HISAT2 on multiple samples

Hey,

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.

Cheers!

rna-seq
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updated by swbarnes2 swbarnes2 • written by Sammy • Sammy

1 answer

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.

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written by swbarnes2 swbarnes2

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