Hi, For alignment, I want to use HISAT2. so for indexing, I download "genome_tran(4.2 GB)" file from indexes section of HISAT 2 website. after download, I extracted that and this folder includes 10 files that they are:
genome_tran.1.ht2 , genome_tran.2.ht2, genome_tran.3.ht2, genome_tran.4.ht2, genome_tran.5.ht2, genome_tran.6.ht2, genome_tran.7.ht2, genome_tran.8.ht2, hg38_ucsc.annotated.gtf, make_h38_tran.sh.
Now, for alignment of my 8 RNA-seq files, I have to use below command based on hisat2 manual:
hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | —sra-acc <SRA accession number>} [-S <hit>]
my problem is that I dont know which file from "genome_tran(4.2 GB)" must use instead of <hisat2-idx> in hisat2 command. "genome_tran.1.ht2" or "genome_tran.2.ht2" or "genome_tran.3.ht2", or ....?
I appreciate if anybody share his/her comment with me. Best Regards, Mohammad
You need the base name, so genome_tran.