vdjtools
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mikessh
Post-analysis of immune repertoire sequencing data
Hi Mike, My question also concerns the Cluster samples command; I don't get any of the txt.files.. I've been doing the same as with the other analyses- so I don't...
Hi, I ran this command to draw the diagram: `java -jar /data/biosoft/vdjtools-1.2.1/vdjtools-1.2.1.jar OverlapPair -p --plot-type png input4VDJtools_SRR7191916.txt input4VDJtools_SRR7191918.txt out1618`  You can see that the image and...
`Sat May 28 22:32:30 GMT+08:00 2022 SegmentUsage] Processing sample ERR3445170.clonotypes.TRB [RUtil] Executing Rscript vexpr_plot.r ./results/desease_state.segments.wt.V.txt 57 0 1 FALSE ./results/desease_state.segments.wt.V.pdf [ERROR] Loading required package: gplots Warning message: In library(package, lib.loc...
Hi, I find a bug of OverlapPair: div1 and div2 are wrong when 'overlap type' isn't 'nt'. Here is an example: java -jar vdjtools.jar OverlapPair -i aa sample1.txt sample2.txt aa/result...
Hello, I would like to know if there is a way to analyse TCRbeta repertoire data with VDJtools taking into account the effects of batch sequencing, considering that my experimental...
Failing to run the main vdjtools-1.2.1.jar, getting the following error: C:\Users\Tom>java -version java version "17.0.2" 2022-01-18 LTS Java(TM) SE Runtime Environment (build 17.0.2+8-LTS-86) Java HotSpot(TM) 64-Bit Server VM (build 17.0.2+8-LTS-86,...
hi, We could like to convert the immunoseq file into vdjtool file. the test file( immunoseq_1.txt) can work.But it has an error when it converting the work flie. [Fri Apr...
Hello mikessh, Thank you for developing so nice software! I tried to install vdjtools in my ubuntu 18.04.5. My R version is 4.1.3. It said: "FAILED to install circlize" Thank...
Sorry to bother you, i run the code as following, Want to know how I should solve it? Thanks! the metadeata.txt with three cols: file_name sample_id and group. java -Xmx4G...
