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Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine

Genomic Interactive Visualization Engine
https://www.givengine.org/
Apache License 2.0
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Custom annotation #26

Open azkalot1 opened 6 years ago

azkalot1 commented 6 years ago

Hi, I have a problem with using custom reference genome and annotation What I did is: bash initial_ref.sh -u root -p Admin2015 -r TestRef -s "Test ref" -c test -f /home/test/test_cytoband.txt bash add_trackGroup.sh -u root -p Admin2015 -r TestRef -g "genes" -l "Known Genes" -o 1 -s 0 bash add_geneAnnot.sh -u root -p Admin2015 -r TestRef -t "knownGene" -g "genes" -l "UCSC known genes annotation" -s "UCSC Genes" -o 1 -v full -f /home/test/vienna_annotations_ucsc.txt

(I include a subset from annotations file and cytoband) test_cytoband.txt annotations_ucsc.txt

but when I open give, I see the following - only part of genes are loading screenshot from 2018-02-27 17-10-48 screenshot from 2018-02-27 17-10-39

I found a following line in givdata/partialNames.php "((SELECT * FROM `knownGene` WHERE `chrom` NOT LIKE '%_%') AS `kGFilter`" Does it meant that annotation can only be added with -t "knownGene" flag? But even if so, is should be a problem in my case, since I added as "knownGene". I tried to add annotation with different flag -t, I had the same error (Most surprisingly, I have exactly one gene on Chr1)

What can be a problem in this case?

caoxiaoyi03 commented 6 years ago

It appears that in the Chr1 region there is indeed only one gene, so the lower panel should be expected. For the upper panel this is indeed weird. Do you have a file with genes on Chr2, with some overlapping with Chr2:11000000-14000000 that we can test?

The problem with partialNames.php is used to provide gene name candidates and convert them to corresponding coordinates. While we are working on it to provide better feedback when such function is not supported (it needs several tables on back end and would probably be unavailable on custom references), it should not affect the browser display.

azkalot1 commented 6 years ago

Even for other regions on Chr1 - this first gene is the only one shown on Chr1 (even if I zoom out)

viennaFiltered_annotation.txt Here is my full annotation (in a slightly different format, but I converted it before importing to GIVE)

caoxiaoyi03 commented 6 years ago

I think the BED display should be fixed by now. gene-coor-input element has also been updated and is awaiting documentation.