I have my own genome fasta file containing 1 chromosome with a modified
header so that it looks like:


I did a FASTQ mapping on it via the galaxy interface and now I end up with
a bam file:

9 Bowtie2 on data 6, data 8, and data 7: aligned reads
1.2 GB
format bam
database ?

I use the visualize button to start the visualization of the dataset. I
chose trackster, And view it in a new visualization. I use my fasta file as
a reference genome:

NameKeyNumber of chroms/contigsSTPmg315STPmg315_v11

But then I get the error:
Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len ,
No such file or directory
I looked into the /chrom/ folder and of course ? does not exist. I am
currently running
python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/
But this ofcourse downloads only known genomes and their chr. information.
As I have my own genome I was curious how to continue with this.

I manually created a file in the /chrom/so that it looks like this:
*head STPmg315.len *

chr1 1900521

but no luck so far. What else do I have to do to make it work?


The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


To search Galaxy mailing lists use the unified search at:


Reply via email to