Question: Output files: "genome.*.bt2" file. What is it?
gravatar for jgcyeoh
4.4 years ago by
United Kingdom
jgcyeoh0 wrote:

Hi everyone,

I ran Bowtie2, mapping my MiSeq reads against a plasmid (8kb) I had to find out if there was any matches. Instead of the usual % matches, the output I got was:

Settings: Output files: "genome.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default

I had to change the reference genome to 'one from history' and selected the plasmid sequence.

Am I doing this right? How do I open this file?

Many thanks!


alignment bowtie • 2.7k views
ADD COMMENTlink modified 4.3 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by jgcyeoh0
gravatar for Jennifer Hillman Jackson
4.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Files named like "genome.*.bt2" are index files for this tool. To use a Custom reference genome in Galaxy, provide a fasta dataset - the option that you switched to. Full instructions are here:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 4.3 years ago by Jennifer Hillman Jackson25k
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