I'm totally new with Bowtie.
I have mate pair reads and I would like to filtered those that have a precise orientation.
Here is the command line I used :
bowtie2 PG21 -p 12 -q -1 MP1.fastq -2 MP2.fastq -phred33-quals -minins 1500 -maxins 2500 -no-mixed -no-dovetail -no-contain -no-overlap -rf -al-con reads_aligned_Rconcordant.fa
My problem is everything seems to be ok except that the fasta output file is empty…
Can you help me ? What did I do wrong ?
How can I get the reads sequences that aligned the way I want ?
Thank you in advance for your help.
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