vdjtools
vdjtools copied to clipboard
mikessh
Post-analysis of immune repertoire sequencing data
Dear Mikhail and Team, I couldn´t find the **vdjtools.jar** file in any of the newer VDJtools bundles. Thankful for any help.
Hello, I read the Testclusters function of VDJtools in your website (https://vdjtools-doc.readthedocs.io/en/master/overlap.html), and I don't get the meaning of the result. What is the permutaion rate of each group, and...
Hi there! I have been dealing with this error, but I have no idea what is it and how to solve it. First I thought it was because the sequence...
Dear Dr. Shugay, Found another bug in TrackClonotypes calculations. In Clonotype tracking stackplot, the "color" and "Clonotype CDR3 amino acid sequence" position is based on the "PEAK" data from "tracking.strict.table.collapsed.txt"...
I would like to use the PlotFancySpectratype function to look at TRD sequences. However, many of the CDR3 lengths are >69nt. At the moment it appears all of the lengths>69nts...
Hello, In the diversity statistics functions in the library - I see that the function being used is the DxxIndex - rather than the D50Index. This should mean that it...
Hey everyone. I am trying to load my single cell TCR seq data (10x) but I dont see the format being supported. Any suggestions?
Hi Mikessh, Thanks for this wonder tool. I'm trying to do CalcBasicStats from TRUST4 output directly, I couldn't use "Convert" because there's no option "-S" for TRUST4. I'm getting following...
Hello, I have recently started using VDJTools. I used JoinSample to create joint clonotype abundance table. I am trying to understand the following: - How the frequency is being calculated...
Hi, I am trying to run the 'intersect_pair_scatter.r' from the 'OverlapPair' module with some modifications to the script. I uncommented the first line in the script as suggested. However, I...
