Question: (Closed) Bowtie2-2.2.5 map error
0
gravatar for kvc0004
3.8 years ago by
kvc00040
United States
kvc00040 wrote:

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

 

next-gen assembly • 1.2k views
ADD COMMENTlink modified 3.8 years ago by h.mon24k • written 3.8 years ago by kvc00040

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.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Daniel Swan13k

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.

ADD REPLYlink written 3.8 years ago by Michael Dondrup46k
1
gravatar for h.mon
3.8 years ago by
h.mon24k
Brazil
h.mon24k wrote:

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
ADD COMMENTlink written 3.8 years ago by h.mon24k
0
gravatar for geek_y
3.8 years ago by
geek_y9.4k
Barcelona/CRG/London/Imperial
geek_y9.4k wrote:

What is "less ‘which map-bowtie2-markduplicates.sh‘" ? this does not make any sense, at least to me. Which tutorial are u following ?

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by geek_y9.4k
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