Hello,
I am mapping paired-end reads from two files per lane, with the following Bowtie command line:
./bowtie -t -v 2 -p 8 -m 1 --solexa-quals mm9 -1 filename1.fastq -2 filename2.fastq outputfilename.map
The program processed 200 million reads in 9 hours, but as a result only about 1% of them mapped. (I expect ~80% reads to be mapped for this experiment). It is very time-consuming to play with the Bowtie parameters for such large files, so I ask for your help.
Any ideas what goes wrong?
Thank you!
I am mapping paired-end reads from two files per lane, with the following Bowtie command line:
./bowtie -t -v 2 -p 8 -m 1 --solexa-quals mm9 -1 filename1.fastq -2 filename2.fastq outputfilename.map
The program processed 200 million reads in 9 hours, but as a result only about 1% of them mapped. (I expect ~80% reads to be mapped for this experiment). It is very time-consuming to play with the Bowtie parameters for such large files, so I ask for your help.
Any ideas what goes wrong?
Thank you!
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