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