Question: Wiggle file (from MIRA coverage) not visualizing?
1
gravatar for vebaev
3 months ago by
vebaev120
Bulgaria
vebaev120 wrote:

I have a Wiggle file from Mirra assembler (mapping mode with reference virus genome), the reference genome is virus and it is ~400nt. My Wiggle file looks like and is 93 lines:

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

But when I create a Visualization with the virus genome and add this file It says cannot be visualized due to error.

wiggle visualizing mira • 114 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson22k • written 3 months ago by vebaev120

Hm.... I got same error trying ti visualize SAM file from bowtie1

ADD REPLYlink written 3 months ago by vebaev120
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson22k 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:

Item to check:

  1. Confirm that the data is all mapped with respect to this exact custom reference genome fasta dataset.
  2. 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
  3. 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 COMMENTlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson22k

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 REPLYlink written 3 months ago by vebaev120
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