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rna seq bowtie couldn't find index files

Hello guys

I am aware that many doubts in the similar contexts have been cleared here. I have been all those discussion forums.Yet I couldn't solve the issue.

I am trying to run the tophat and this following error comes up:

prasanth@prasanth-ngs:~/Desktop/myecoli-rna seq/data $ tophat2  ~/Desktop/myecoli-rna seq/referecoli -0 ~/Desktop/myecoli-rna seq/alignment  exponential.fastq stationary.fastq 

[2016-12-21 16:21:52] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2016-12-21 16:21:52] Checking for Bowtie
          Bowtie version:    2.1.0.0
[2016-12-21 16:21:52] Checking for Samtools
        Samtools version:    0.1.19.0
[2016-12-21 16:21:52] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (/home/prasanth/Desktop/myecoli-rna.*.bt2)
prasanth@prasanth-ngs:~/Desktop/myecoli-rna seq/data $ tophat 
bowite/                   referecoli.bt2.1.bt2      referecoli.bt2.4.bt2      referecoli.fasta          typescript
exponential.fastq         referecoli.bt2.2.bt2      referecoli.bt2.rev.1.bt2  stationary.fastq          
fastqc/                   referecoli.bt2.3.bt2      referecoli.bt2.rev.2.bt2  tophat_out/

Guys, once again for repeating the question, but I have tried all my options and this is my only option left to post it here..

Thank you for your time.

tophat bowtie rna-seq
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updated by Ram Ram • written by prasanthgopinathangs • prasanthgopinathangs

Please read the how-to posts before writing a post. This is not a "Tool" post, it's a "Question". I'm making the necessary changes now.

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written by Ram Ram

When you say "I have tried all my options", what exactly have you tried? Please give us the commands you ran to try and solve this.

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written by Ram Ram

I see your bowtie index files are named as referecoli. The problem could be due to the space in foldername "myecoli-rna seq", as the program consider it as 2 different folders as myecoli-rna and seq, so it is searching for myecoli-rna.*.bt2 as index file

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written by sysbiocoder sysbiocoder

That's very likely the cause. Just avoid spaces in your directory and filenames.

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written by WouterDeCoster WouterDeCoster

The output folder you specified should be followed by "-o" not "-0" and avoid spaces in directory/filenames. 

~/Desktop/myecoli-rna seq/referecoli should be written as ~/Desktop/myecoli-rna\ seq/referecoli
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written by Arup Ghosh Arup Ghosh

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