search

elsiklab / fastloader

A JBrowse plugin for working with variable template parameters in BAM, VCF, tabix (the broken up index is "faster", hence fastloader)
0 stars 0 forks source link

How to set color according to SNP effect #3

Closed shenweima closed 7 years ago

shenweima commented 7 years ago

I have got the SNP annotation using snpEff. I want to set color according to SNP effect.But I don't know how to set. This is my setting { "storeClass" : "JBrowse/Store/SeqFeature/VCFTabix", "urlTemplate" : "tracks/marker/90k_snp.eff.vcf.gz", "tbiUrlTemplate":"tracks/marker/90k_snp.eff.vcf.gz.tbi", "label" : "wheat_90K", "category" : "Marker", "type" : "JBrowse/View/Track/CanvasVariants", "key" : "wheat_90K" }, I have added the FastLoader to my plugins files. But I don't know how to make it work，can you help me? The below website is what I want. The snp have colored according its effect. https://dubcovskylab.ucdavis.edu/jbrowse/?data=data%2Fjson%2Fiwgsc-2BS&loc=IWGSC_CSS_2BS_scaff_1562879%3A1..3416&tracks=tgacannot%2Cmipsannot%2CsnpsgenomeHC%2CcadsnpsHC%2Cmulticontigs%2Ccadmulticontigs%2Cblast%2CDNA&highlight=IWGSC_CSS_2BS_scaff_1562879%3A1..960&addFeatures=%5B%7B%22seq_id%22%3A%22IWGSC_CSS_2BS_scaff_1562879%22%2C%20%22start%22%3A%201%2C%20%22end%22%3A%20960%2C%20%22name%22%3A%20%22MyBLASTHit_1%22%2C%20%22description%22%20%3A%20%22evalue%200.0%22%7D%5D&addTracks=%5B%7B%22label%22%3A%22blast%22%2C%22store%22%3A%22url%22%2C%22type%22%3A%22JBrowse%2FView%2FTrack%2FHTMLFeatures%22%2C%20%22key%22%3A%22BlastHSP%20Results%22%7D%5D%0A

cmdcolin commented 7 years ago

Technically the coloring had nothing to do with fastloader. I saw you filed a duplicate issue on the jbrowse forum so I'll close this for now