Serghei Mangul

ERROR : span is too small

2

Hi, i am getting this error: Correcting for GC bias... Error in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, : span is too small Calls: loadReadCountsFromWig ->...

problem running vdjer on bam file from GTEx

6

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...

check if the extension is bam if bam was selected right now if i run ~/anaconda2/bin/python imrep.py --noCast example/toyExample.fastq test this error Traceback (most recent call last): File "imrep.py", line...

to report CDR3 supported by a single read i need to run : python ../../../../imrep/imrep.py -f -1 unmappedExample_after_lostRepeat.fasta test.cdr3

Temp solution sed 's/\t/;/g' PT0112-baseline.sort_input.no.OverlapStep.cdr3 >PT0112-baseline.sort_input.no.OverlapStep.new-format.cdr3

- Reads vs number clonotypes. TO provide practical recommendations for user -Capture recapture. -Paired ends to vdj and partial.

bug

2

Hi Igor, This is the bug i have noticed CQQYGRGSTF IGH 2 TRDV3,TRAV12,TRAV13 NA TRDV3,TRAV12,TRAV13 column 2 says it is IGH but this is actually TRD Serghei

Let's report in the default mode for each CDR3 - the average length of overlap for particular CDR3 - flag if the CDR3 was assembled from 2 reads or one...

DNA seq of CDR3

2

Do you think we can report the DNA Seq of CDR3 And maybe map the reads onto those to better quantify the CDR3s? What do you think?

Error when running

5

Hi Jason, Thanks for doing a great job making a USABLE version of the software. I followed your instruction. Unfortunately, i am still getting an error "perl: symbol lookup error:...