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Cannot Find Bowtie Index Files HELP, PLEASE
Hello, I am trying to learn how to analyze our mouse liver RNA-seq data using the tuxedo suite pipeline. I am also a novice when it comes to using unix commands. Anyways, I am at the stage where I need to run TopHat, but I keep getting the following error:
~/Desktop$ tophat2 '/home/shibin/Desktop/mm10' wt01.fastq,wt02.fastq,wt03.fastq
[2018-08-29 14:09:23] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-08-29 14:09:23] Checking for Bowtie
Bowtie version: 2.3.4.1
[2018-08-29 14:09:23] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (/home/shibin/Desktop/mm10.*.bt2l)
I have already downloaded the mm10 reference genome from Bowtie's website. I checked it with the bowtie2-inspect command, and it was fine. I pasted the verified path to reference genome (and my read.fq file names); however, bowtie cannot find my index files.
I do have each folder/directory (bowtie, tophat, mm10) in the "Desktop."
Help is really appreciated.
~/Desktop$ tophat2 '/home/shibin/Desktop/mm10' wt01.fastq,wt02.fastq,wt03.fastq
[2018-08-29 14:09:23] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-08-29 14:09:23] Checking for Bowtie
Bowtie version: 2.3.4.1
[2018-08-29 14:09:23] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (/home/shibin/Desktop/mm10.*.bt2l)
I have already downloaded the mm10 reference genome from Bowtie's website. I checked it with the bowtie2-inspect command, and it was fine. I pasted the verified path to reference genome (and my read.fq file names); however, bowtie cannot find my index files.
I do have each folder/directory (bowtie, tophat, mm10) in the "Desktop."
Help is really appreciated.