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 :
I attempted and the command was not found.
I then entered:
less ‘which map-bowtie2-markduplicates.sh‘
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!