Wiggle file (from MIRA coverage) not visualizing?

track type=wiggle_0 name="name" description="name strain: ReferenceStrain Mapped strain(s): " visibility=full autoScale=off viewLimits=0:151 color=0,200,100 maxHeightPixels=100:50:20 graphType=bar priority=30 fixedStep chrom=name start=1 step=4 span=4 2 19 29 47 77

22 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There could be a formatting problem with the custom genome, or it did not index correctly, or it is not the exact genome/transcriptome/other fasta file/dataset the problematic display data was mapped against.

Custom genome format rules:

Wiki: https://wiki.galaxyproject.org/Learn/CustomGenomes#Format
See generalized details near end of post: https://biostar.usegalaxy.org/p/14777/

Item to check:

Confirm that the data is all mapped with respect to this exact custom reference genome fasta dataset.
Verify format and database assignment
- Title line has identifier only (no description)
- Identifier names are distinct, nucleotide sequence lines are wrapped
- Datasets have the Custom Genome Build assigned as the database
Delete the prior Custom Genome Build index (User -> Custom Genomes) and create it again. Then try Trackster again.

Item 3 assumes that item 1 checked out. If it didn't, then the genome mismatch needs to be corrected. If any changes are made for item 2, the custom build should be recreated (item 3) and the analysis will need to be started over from the beginning or conflicts will continue (re-run from the mapping step forward).

Thanks, Jen, Galaxy team

ADD COMMENT • link modified 22 months ago • written 22 months ago by Jennifer Hillman Jackson ♦ 25k

Dear Jen, I think there is something wrong or I'm doing things in a wrong way. Just to check if I can visualize a track I create new Track Browser (with all_fasta genome of tomato, I had added before), I downloaded the official GFF3 of the same tomato genome and assigned as the database the all_fasta genome).

Upon loading (flashing yellow) line the track again ended as the previous attempt with red line "could not load due to error" After that I have found I had in the history a double job on the GFF3 with red error saying:

Dataset 58: ITAG2.4_gene_models.gff3

Tool execution generated the following error message:
/export/galaxy-central/database/job_working_directory/000/222/tool_script.sh: line 9: bedtools: command not found
/export/galaxy-central/database/job_working_directory/000/222/tool_script.sh: line 9: bedGraphToBigWig: command not found

enter image description here

ADD REPLY • link written 22 months ago by vebaev • 130

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