Plotting large regions using local bam file with jbrowse/img

[kcleal]

Im trying to plot a large region view using jbrowse/img. I have been trying this with:

jb2export --fasta $HG19 --bam chr1.bam --loc chr1:10000-30000 --out jbrowse.png --configtracks bam force:true --config alignments.config

The config file I made was:

{
  "trackId": "bam",
  "name": "bam",
  "assemblyNames": ["hg19"],
  "type": "AlignmentsTrack",
  "adapter": {
    "type": "BamAdapter",
    "bamLocation": {
      "uri": "chr1.bam"
    },
    "index": {
      "location": {
        "uri": "chr1.bam.bai"
      }
    }
  }
}

However I get an error message Error: Could not resolve identifier "bam"

How can I fix this? Thanks

[cmdcolin]

I might have to look into this, I thought something like force:true just on the --bam flag would work but it throws an error

jb2export --fasta $HG19 --bam chr1.bam force:true --loc chr1:10000-30000 --out jbrowse.png
[
  TypeError: self.PileupDisplay.setUserFeatureScreenDensity is not a function
      at Object.setUserFeatureScreenDensity (/home/cdiesh/.fnm/node-versions/v18.12.1/installation/lib/node_modules/@jbrowse/img/node_modules/@jbrowse/plugin-alignments/dist/LinearAlignmentsDisplay/models/model.js:196:32)
      at executeAction (/home/cdiesh/.fnm/node-versions/v18.12.1/installation/lib/node_modules/@jbrowse/img/node_modules/mobx/dist/mobx.cjs.development.js:1257:15)
      at bound setUserFeatureScreenDensity (/home/cdiesh/.fnm/node-versions/v18.12.1/installation/lib/node_modules/@jbrowse/img/node_modules/mobx/dist/mobx.cjs.deve
...

I'll check into it and let you know. super impressed by the gw tool, i imagine @jbrowse/img will probably get trounced by it but would be fun to compare

[kcleal]

Hi @cmdcolin, thanks for the quick response - and your nice comment about gw. Im trying to compare as many tools as possible so any help would be much appreciated, thanks!

[cmdcolin]

@kcleal i think the force flag should work now, can reinstall with npm install -g @jbrowse/img for latest. i tried plotting some largish region of long reads, 900kb

jb2export --fasta http://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz --cram http://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/skbr3/skbr3.ont.sort.mod.cram force:true --loc 1:1,000,000-1,900,000

with larger region it is a out of memory. might need to add node env variables to give it more memory for these cases

the --fasta and --cram/--bam flags should work on local files as well as urls. plotting large e.g. megabase scale regions with alignments is definitely an interesting challenge :) i normally conceive of people creating e.g. a bigwig or some reduced version of the data but it is often interesting to get the raw data too

[cmdcolin]

also just for reference, using --configtracks is used for picking specific trackIds out of a config.json (which is normally created by the @jbrowse/cli of the web, and contains assemblies, tracks, etc.)

[kcleal]

Thanks so much! I will give it a try on Friday Get Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Colin Diesh ***@***.***> Sent: Wednesday, November 23, 2022 2:38:47 AM To: GMOD/jbrowse-components ***@***.***> Cc: Kez Cleal ***@***.***>; Mention ***@***.***> Subject: Re: [GMOD/jbrowse-components] Plotting large regions using local bam file with jbrowse/img (Discussion #3331) External email to Cardiff University - Take care when replying/opening attachments or links. Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni. also just for reference, using --configtracks is used for picking specific trackIds out of a config.json (which is normally created by the @jbrowse/cli of the web, and contains assemblies, tracks, etc.) — Reply to this email directly, view it on GitHub<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Fdiscussions%2F3331%23discussioncomment-4211968&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C679ef4c20eff4716f11808daccfbd9c8%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638047679301005528%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2FCLDtRfyDF9k5yl%2FX049fsUWrbtRZiJThLa0mqJt%2FY4%3D&reserved=0>, or unsubscribe<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAKIBQHP6YSYTJBOHY7RT77LWJV7TPANCNFSM6AAAAAASBJXTIQ&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C679ef4c20eff4716f11808daccfbd9c8%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638047679301005528%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vIg7mfKG5ELZ2QLOZfwiFAa%2FexE04ZW9LEHodLTAyu0%3D&reserved=0>. You are receiving this because you were mentioned.Message ID: ***@***.***>