Bowtie Issues

Question

[Namibia]

I want to use BOWTIE for alligning reads in a DNA sequence database. Can anybody help me,

what formats it accepts for:

1) DNA sequence database.

2) Database which contains 35 bps query reads.

And I want to find allignments allowing 2 mismatches and want to get report in my file system (not in display). Can anybody help me in what allignment mode or command I have to run.

Sorry, I am new in bioinformatics, so can't able to get much technical term.

Thanks in advance.

[Sean Davis]

Though I have no doubt that you will get your task accomplished, you should find a local bioinformatics person with NGS experience to work through your first set of data with you.

Answer 1

[Istvan Albert]

Work through the Bowtie tutorial below. All the data are included in the source distribution.

http://bowtie-bio.sourceforge.net/tutorial.shtml

then move onto the manual:

http://bowtie-bio.sourceforge.net/manual.shtml