Trackster Error chrom/?.len , No such file or directory
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
You'll need to set your dataset's database/dbkey to your custom reference genome before you can visualize it. We have enhancements planned so that this error doesn't happen in the future. Best, J. On Dec 5, 2013, at 7:56 AM, Jasper Jan Koehorst <jasper.koehorst@wur.nl> wrote:
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:
Name Key Number of chroms/contigs STPmg315 STPmg315_v1 1
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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participants (2)
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Jasper Jan Koehorst -
Jeremy Goecks