Colin Diesh
Colin Diesh
Reported by user on gitter ``` NC_007112.7 BestRefSeq gene 24355021 24360249 . + . ID=gene-rps3a;Dbxref=GeneID:337240,ZFIN:ZDB-GENE-030131-9184;Name=rps3a;description=ribosomal protein S3A;gbkey=Gene;gene=rps3a;gene_biotype=protein_coding;gene_synonym=fb02h01,rpS3Ae,wu:fb02h01,zgc:73195,zgc:86672 NC_007112.7 BestRefSeq regulatory_region 24355021 24355520 . + . ID=promoter-rna-NM_200059.2;Parent=rna-NM_200059.2;Dbxref=GeneID:337240,Genbank:NM_200059.2,ZFIN:ZDB-GENE-030131-9184;Name=NM_200059.2;gbkey=promoter;gene=rps3a;product=ribosomal protein S3A;transcript_id=NM_200059.2;regulatory_class=promoter NC_007112.7 BestRefSeq...
Storing the file handles in indexed db is allowed and survives refresh https://developer.chrome.com/docs/capabilities/web-apis/file-system-access#storing_file_handles_or_directory_handles_in_indexeddb
I believe UCSC autogenerates a restriction enzyme track @scottcain I believe also made a plugin for this at one point in jbrowse 1  Above image from UCSC aardvark assembly...
Currently you can mouseover a squiggle, but it would be nice to see the exact reads connected by the squiggle visually
Xref https://github.com/GMOD/jbrowse-components/discussions/4714
Currently paired end reads are only rendered in the breakpoint split view if they are identified as NOT "read mapped in proper pair" (sam flag 0x02) this appears to miss...
Currently automatically does a "split level" breakpoint split view Might require popping up a context menu from feature click This might be good to do anyways as there are multiple...
HSL hue values go beyond 255 and wrap around to 0, making it hard to tell what values are actually large or small Properly, it should estimate average and range...
- color which parts of the read sequence are clipping/insertions, mark deletions, etc. - add coordinate information (similar to the basefeaturedetail sequence panel like #4399 )