Error parsing ImmunoSeq files

[ccasar]

I've setup a local vdjdb-server and whenever I try to upload a sample file from ImmunoSeq the upload immediately throws an error:

[info] c.v.com - User vdjviz1@vdjviz.com: Error while rendering sample sample1

What kind of ImmunoSeq format does the server expect?

I tried ImmunoSeq v2 and v3, where the file headers are:

v2: nucleotide aminoAcid count (templates) frequencyCount (%) cdr3Length vMaxResolved vFamilyName vGeneName vGeneAllele vFamilyTies vGeneNameTies vGeneAlleleTies dMaxResolved dFamilyName dGeneName dGeneAllele dFamilyTies dGeneNameTies dGeneAlleleTies jMaxResolved jFamilyName jGeneName jGeneAllele jFamilyTies jGeneNameTies jGeneAlleleTies vDeletion n1Insertion d5Deletion d3Deletion n2Insertion jDeletion vIndex n1Index dIndex n2Index jIndex estimatedNumberGenomes sequenceStatus cloneResolved vOrphon dOrphon jOrphon vFunction dFunction jFunction fractionNucleated

v3: nucleotide aminoAcid count (templates/reads) frequencyCount (%) cdr3Length vMaxResolved vFamilyName vGeneName vGeneAllele vFamilyTies vGeneNameTies vGeneAlleleTies dMaxResolved dFamilyName dGeneName dGeneAllele dFamilyTies dGeneNameTies dGeneAlleleTies jMaxResolved jFamilyName jGeneName jGeneAllele jFamilyTies jGeneNameTies jGeneAlleleTies vDeletion n1Insertion d5Deletion d3Deletion n2Insertion jDeletion vIndex n1Index dIndex n2Index jIndex estimatedNumberGenomes sequenceStatus cloneResolved vOrphon dOrphon jOrphon vFunction dFunction jFunction fractionNucleated vAlignLength vAlignSubstitutionCount vAlignSubstitutionIndexes vAlignSubstitutionGeneThreePrimeIndexes vSeqWithMutations

Or might there be something else wrong?

[mikessh]

Hello, this must be a problem with vdjtools parsing immunoseq files. Your file appears to be in v2 format. I've just got latest sample exports in both immunoseq formats and I'm going to fix it.

The corresponding vdjtools issue is: https://github.com/mikessh/vdjtools/issues/58

[ccasar]

Hi, actually I was able to convert my current ImmunoSeq V3 files with vdjtools

vdjtools.jar Convert -S immunoseq

to generate vdj formatted files. But once I tried to upload them, I still got the same error.

[mikessh]

Hi, can you please test the latest release of VDJtools?

https://github.com/mikessh/vdjtools/releases/tag/1.1.2

Your option should be -S immunoseqv2 based on the column names you've provided. Don't use the files converted with Immunoseq V3, these might be converted incorrectly.

I'll update vdjdb-standalone (https://github.com/antigenomics/vdjdb-standalone) and vdjdb-server asap. Note that you can upload converted files (i.e. in VDJtools format) to vdjdb-server and vdjdb-standalone for analysis.

Please let me know if this helps.

[ccasar]

Hi, actually I just realized, I opened this issue for the wrong project...I meant to open it for vdj-viz. Should I reopen the issue over there?

Nonetheless I went back to immunoSEQ and exported our samples via 'Export Sample' (A) and 'Export Sample (v2)' (B) from the Project Overview.

I can't upload any of those samples via the vdjviz webinterface. When trying to convert files from A or B via vdjtools 1.1.2, only files from B with -S immunoseqv2 are successful all other combinations of A/B and -S immunoseq(v2) fail. But even with the converted vdj files, I still receive an immediate error when trying to upload them via the vdjviz webinterface.

Additionally I tried your example data, but the sample rendering fails for this dataset as well.

[mikessh]

VDJviz and VDJdb run with the same back-end. We'll update both of them with the new version of VDJtools that handles ImmunoSEQ parsing soon. As for now, you can get the latest version of VDJtools using the link I've provided in previous comment, convert all your files to VDJtools format and upload them to VDJviz/VDJdb using "VDJtools" as the input format.