Dear all,
I am wondering whether there is a way to enter the quality scores from a read directly into the command line when running bowtie rather than open the actual read file.
It is possible to do something like this (for e.g.):
bowtie -f Ref_Genome -c ATTTGCTATGCATCT out.txt
but I would like to do something like this:
bowtie -q Ref_Genome -c ATTTGCTATGCATCT -xxx IJEHHHEFFFDDDED out.txt
I know that I can simply write this information to a file and give the file name as the input data, but I am trying to run bowtie as a subprocess from a Python script and so would prefer to avoid writing a new read file for each alignment.
Many thanks for any help,
Andrew
I am wondering whether there is a way to enter the quality scores from a read directly into the command line when running bowtie rather than open the actual read file.
It is possible to do something like this (for e.g.):
bowtie -f Ref_Genome -c ATTTGCTATGCATCT out.txt
but I would like to do something like this:
bowtie -q Ref_Genome -c ATTTGCTATGCATCT -xxx IJEHHHEFFFDDDED out.txt
I know that I can simply write this information to a file and give the file name as the input data, but I am trying to run bowtie as a subprocess from a Python script and so would prefer to avoid writing a new read file for each alignment.
Many thanks for any help,
Andrew
