imrep

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unmapped reads in fastq/fasta format and pair-end data

4

Hello, I want to try `imrep` with my RNA-seq data. I've aligned the `fastq` to genome with `STAR`, and saved the unmapped reads in `fastq` format (using `--outReadsUnmapped Fastx`). As...

YiweiNiu

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

smangul1

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

smangul1

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

smangul1

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

smangul1

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...

smangul1

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?

smangul1