Hello,
I have read through manuals and look for many days, but I cannot find the solution to this error. I am trying to map my contigs back to my assembly using bowtie2-2.2.5. I am able to use the bowtie-build command, but the next command in the tutorial for concoct called for:
map-bowtie2-markduplicates.sh
I attempted and the command was not found. I then entered:
less 'which map-bowtie2-markduplicates.sh'
and received:
map-bowtie2-markduplicates.sh: No such file or directory
I followed the instructions for install and looked through all the files manually. I tried to use the bowtie2 forum and I did not have access to ask questions. I am so frustrated. please help!
Thank you
2 answers
This is in no way an error with Bowtie2, there is no "map-bowtie2-markduplicates.sh" script on the Bowtie2 package.
You are trying to run an script you do not have - or not added to your PATH - from a tutorial which we don't know (is there a link?) so we can't help much. But I guess you need to add this script (probably install the whole CONCOT package) and add them to your PATH:
export PATH=/path/to/concot:/path/to/concot/scripts:$PATH
What is "less ‘which map-bowtie2-markduplicates.sh‘" ? this does not make any sense, at least to me. Which tutorial are u following ?
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Hello kvc0004!
We believe that this post does not fit the main topic of this site, as this relates to not being able to find an executable on your
$PATH. Consequently it is not a bioinformatics question despite involving a bioinformatics tool.For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
The first idea I have to google the file name, voila: https://github.com/BinPro/CONCOCT/blob/master/scripts/map-bowtie2-markduplicates.sh , not quite sure what is difficult about this.
You also mentioned concoct, you need to clone the repository and install the script.