Hi all,
I have some 100bp PE reads. I combined my left.fa and right.fa files into one file 'both.fa' and tried aligning these reads to my reference using Tophat/Bowtie.
Alignment ran to completion without reporting any errors, however the accepted_hits.bam output was not usable by cufflinks.
First I got an error saying that the file was not sorted.
After sorting I got an error saying "EOF marker is absent" and that the file is not a BAM file.
Does anyone know:
1. can Bowtie accept both left and right reads in the same file?
2. would this cause sorting/header errors?
I have some 100bp PE reads. I combined my left.fa and right.fa files into one file 'both.fa' and tried aligning these reads to my reference using Tophat/Bowtie.
Alignment ran to completion without reporting any errors, however the accepted_hits.bam output was not usable by cufflinks.
First I got an error saying that the file was not sorted.
After sorting I got an error saying "EOF marker is absent" and that the file is not a BAM file.
Does anyone know:
1. can Bowtie accept both left and right reads in the same file?
2. would this cause sorting/header errors?
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