vdjtools

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mikessh

cdr3 from IMGT-highvquest

1

Hi, I found that JUNCTION data has been chosen instead of CDR3_IMGT while converting process. Is there reason why you did this? Thanks

josh4ever

Installing using brew on Mac OSX Sierra, I got the error: ``` ==> Installing mikessh/repseq/vdjtools dependency: r ==> Downloading https://homebrew.bintray.com/bottles/r-3.4.3_1.sierra.bottle.tar.gz ######################################################################## 100.0% ==> Pouring r-3.4.3_1.sierra.bottle.tar.gz Error: The `brew link` step...

markgene

Unable to parse clonotype string ... Attached is the error log. [_vdjtools_error.log](https://github.com/mikessh/vdjtools/files/1665740/_vdjtools_error.log)

IvantheDugtrio

Shared clonotype abundance plot labels up-side-down.

4

as figures below,   NonOverlapping should be in grey which is on the top. looks like it's right in the document sample. 

suntaosimon

Hi, I'm trying to convert some files containing data in the immunoseq format. However, on some files the convert function seems to run fine while on others I'm receiving the...

NDeNeuter

ImmunoSeq parser is treating out-of-frame sequence as in-frame

1

Hi, is the following ImmunoSeq-to-VDJtools conversion correct? 1) I ran the command ``` vdjtools Convert -S ImmunoSeq -m metadata4Convert.txt ./samples/ ``` 2) I am trying to understand how the ImmunoSeq...

malisas

I am running 1) Java/1.8.0_121 2) VDJtools/1.1.5 on a cluster. When I try to use the preprocessing command FilterByFrequency, I receive the error below. I don't see FilterByFrequency in the...

eperry10

Hi, I am plotting the VJ usage of 4 different patients groups, individually. Is it possible to keep the the same colorcode and placement of the TRBV/ TRBJ genes in...

dstatovci

I have tried `Convert \ -S Vidjil sample.vidjil output` But I don't think this is the right command. Please help. thanks!

suntaosimon