Question: Trackster Error Chrom/?.Len , No Such File Or Directory
0
Jasper Jan Koehorst • 20 wrote:
I have my own genome fasta file containing 1 chromosome with a
modified
header so that it looks like:
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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modified 5.0 years ago
by
Jeremy Goecks • 2.2k
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written
5.0 years ago by
Jasper Jan Koehorst • 20
