bowtie1 parameter -k

Question

[biolab]

Hi, everyone, I have a simple question regarding to the -k parameter of bowtie1. The manual states "report up to <int> good alignments per read (default: 1)". If I set -k 1, for a multiple read, is it randomly assigned to a position?
Thank you very much!

Answer 1

[mastal511]

Yes. It just reports the first alignment.

Quote from the bowtie1 manual:

http://bowtie-bio.sourceforge.net/manual.shtml#example-2--k-3

"Leaving the reporting options at their defaults causes bowtie to report the first valid alignment it encounters. Because --best was not specified, we are not guaranteed that bowtie will report the best alignment, and in this case it does not (the 1-mismatch alignment from the previous example would have been better). The default reporting mode is equivalent to -k 1."

[biolab]

Thank you, mastal511. It's very helpful!