Tophat Indexing Help (VM) cmd & bowtie index files

[archaeogen]

Hi everyone,

new to tophat indexing...
I have 2 fastq files and a fa. reference genome and gtf. gene annotations file.
I am trying to use tophat to align the fastq files to the reference genome. I have created an index with bowtie and stored it in /home/guest/Index with the name 'athal'.

I am running tophat from my text editor nano
sh assign.tophat >& com.tophat.log

My nano text editor script is the following.
DATADIR=/file/path/for/fastq files (*not the actual file path name)
WORKDIR=/file/path/for/output/alignment/file*
ANNOT=/file/path/for/gtf/gene annotations*
BWT2IDX=/home/guest/Index/athal (my bowtie index)

tophat -o $WORKDIR -p 10 -G $ANNOT $BWT2IDX $DATADIR/Day16.fastq $DATADIR/Day8.fastq


I get the following errors reported in com.tophat.log

assign.tophat: line 1: Line: command not found
* this is the same for line 2 & 3
Then...
Beginning TopHat run (v2.0.14)
------
checking for Bowtie
Bowtie version: 2.2.5.0
Checking Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (10.*.bt2)

I have seen a previous post that could not locate the bowtie index and followed the steps (I had already put the index file path into a line in the text file) but to no success.

Really at a loss here for answers. Any tips would be amazing!
I am running ubuntu from a virtual machine (Windows 10)

[GenoMax]

1. $WORKDIR needs to be a directory. It appears to be pointing to files as written above. It can be a new name (generally good to put results from a sample in new dir since all TopHat output files for any sample are named the same).

If that is not it then check

2. if TopHat is not in the directory you are running this from them provide the full path to the executable.
3. In case of the index files you need to provide the "basename" of the index. e.g. are your index files named athal.* (then athal would be the base name).