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

>chr1
ATGCATGC....

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?


Thanks,


Jasper
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