The parameter of HISAT2 and samtools

Question

[Evy_00]

Hi all,

I'm a new to RNA-seq and I'm going to use HISAT2 and samtools to analyze my data. I found the method from ref which recommended me to deal with the data like this.

CODE ->

hisat2 -t -p 16 -x <indexPath> -U <fastqFiles> | samtools sort -T <scratchPath> -o <sampleName>.srt.bam -

But I have no idea what the parameters <indexpath> and <scratchpath>mean. Can someone help me to explain the defination or usage of the parameters? It will be better if there's any example. Thanks a lot!

Evy

Answer 1

[jordi.planells]

The -x flag in hisat2 is used to provide an index. Most aligners need an index in order to perform better (faster). So you first need to build an index and the provide the path to where this index is located. To build an index with hisat2 you just need to use the hisat2-build command. See more in the manual. In samtools sort the -T flag is used to specify the folder where temporary files are stored. You can always learn more about the different options each program has in the manual or by typing hisat2/samtools --help.
Hope it helps!
Jordi

[Evy_00]

Thanks! I have processed my data successfully!