Using PET files as SET files in bowtie
Hello - thanks for bowtie - I like it and the output is handy for me to analyse.
I have a bit of odd behavior to report that I can't understand or figure out. I have lots of little contigs (100-1000 bp) that I am aligning against and I have both SET and PET files.
When I align the SET against the short contigs, everything works great. <example command follows>
./bowtie -f shortcontigs_index lane1.fa lane1vreference.map
When I align both files for the PET data, everything works great but obviously my results are strongly biased towards those pairs which are very close together and many of the alignments are rejected because one of the pairs is sticking out into 'space'...
./bowtie -f shortcontigs_index -1 lane1_1.fa -2 lane1_2.fa lane1vreference.map
When I try to use one of the PET files as a singles file, bowtie runs for just a second, usually reporting that one of my reads is less than 2 base pairs long and then quits.
./bowtie -f shortcontigs_index lane1_1.fa lane1vreference.map
Does bowtie somehow detect that the original file is a PET file and will not let me run it by itself?
Hello - thanks for bowtie - I like it and the output is handy for me to analyse.
I have a bit of odd behavior to report that I can't understand or figure out. I have lots of little contigs (100-1000 bp) that I am aligning against and I have both SET and PET files.
When I align the SET against the short contigs, everything works great. <example command follows>
./bowtie -f shortcontigs_index lane1.fa lane1vreference.map
When I align both files for the PET data, everything works great but obviously my results are strongly biased towards those pairs which are very close together and many of the alignments are rejected because one of the pairs is sticking out into 'space'...
./bowtie -f shortcontigs_index -1 lane1_1.fa -2 lane1_2.fa lane1vreference.map
When I try to use one of the PET files as a singles file, bowtie runs for just a second, usually reporting that one of my reads is less than 2 base pairs long and then quits.
./bowtie -f shortcontigs_index lane1_1.fa lane1vreference.map
Does bowtie somehow detect that the original file is a PET file and will not let me run it by itself?
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