vdjer
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mozack
V'DJer - B Cell Receptor Repertoire Reconstruction from short read mRNA-Seq data
The Markdown formatting in the README.md did not render some of the example command lines correctly.
Is there someplace where mouse references and indices compatible with VDJer can be obtained or do I need to just do my best to mimic what you did with the...
Hi everyone, I'm trying to use vdjer on my data. I perform the tutorial, with the data provided in the package and It's working. Problems appears when I tried with...
Hi, I am trying to use **VDJer** to pull out BCR-seq data from sorted and indexed BAM files created by HISAT2 (alignment with hg38 ucsc). However, when I run it,...
Hello, can vdjer work on whole-exome sequencing data? or how to adjust the parameters to make it work for whole-exome sequencing data? Thanks much!
We hard time running the tool for bam file from GTEx project. We use bam files produced by GTEx consortium. Reads were mapped to hg19 using Tophap. Bam files contain...
Here is a simulated IGH sample (using simNGS): [igh.fa.txt](https://github.com/mozack/vdjer/files/805783/igh.fa.txt) - simulated IGH transcripts [r1.fastq.txt](https://github.com/mozack/vdjer/files/805784/r1.fastq.txt) - simulated reads (left pairs) [r2.fastq.txt](https://github.com/mozack/vdjer/files/805785/r2.fastq.txt) - simulated reads (right pairs) The .txt suffix is appended...
Hi, Is there way to extract reads that were successfully assembled by vdjer from the original bam file? I mean the following. I supposed that `vdjer.sam` contains reads that were...
