A small correction that simplifies the process. Please see below.
On 8/6/10 6:24 PM, Jennifer Jackson wrote:
Yes, to do this, create your own reference index, load it into your
history (ftp/http load), and specify that index for mapping.
NGS: Mapping -> Map with Bowtie for Illumina
Will you select a reference genome from your history
or use a built-in index?: "use one from the history"
At this step, select the reference sequence fasta file from your history
and set indexing parameters (all on the same form). No need to pre-index!
So, skip all the this:
You will need the Bowtie distribution to do the indexing. Here is a
to the tutorial help for the process and the source (if you don't have
On 8/6/10 12:42 PM, Antony Jose wrote:
> I am a relatively new user to Galaxy. Of the 21 million mappable
> illumina reads, 17 million mapped to a reference genome. I would like
> to know if the remaining 4 million come from a known contaminating
> sequence for which I have a .txt file. Is there an easy way of doing
> this in Galaxy? Please advice.
> Thank you.
> galaxy-user mailing list