Hi
I recently downloaded Bowtie and tying to align affy sequences. I am still using BLAT for longer sequences, but for short sequences, Bowtie is having clear advantage.
I have a doubt about the default output of bowtie. Field number FOUR(4) gives 0-based offset of the start location of reads on the genome. But it is not showing the location where mapping ends. For example, the BLAT output tells you everything including start, end , length of reads matched, mismatched etc. etc.
What I am assuming that since bowtie does not allow gapped alignment, the end should be equal to ( start+ lenghtOfReads-1). Is it true for the alignment results?
Thanks
Fahim
I recently downloaded Bowtie and tying to align affy sequences. I am still using BLAT for longer sequences, but for short sequences, Bowtie is having clear advantage.
I have a doubt about the default output of bowtie. Field number FOUR(4) gives 0-based offset of the start location of reads on the genome. But it is not showing the location where mapping ends. For example, the BLAT output tells you everything including start, end , length of reads matched, mismatched etc. etc.
What I am assuming that since bowtie does not allow gapped alignment, the end should be equal to ( start+ lenghtOfReads-1). Is it true for the alignment results?
Thanks
Fahim
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