Hi all,
I successfully used bowtie to perform some single end alignments.
Now, I would like to perform some paired-end alignments using bowtie 2, and I am just wondering if I am oblige to use the SAM output format option.
How will be the output if I don't specified this option?
The manual only clearly mention the SAM output format.
What is the best of the two possibilities.
Many thanks
I successfully used bowtie to perform some single end alignments.
Now, I would like to perform some paired-end alignments using bowtie 2, and I am just wondering if I am oblige to use the SAM output format option.
How will be the output if I don't specified this option?
The manual only clearly mention the SAM output format.
What is the best of the two possibilities.
Many thanks
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