Vignettes for capSequm and CCseqBasic

If you face problems in walk-through - report issues to jelena dot telenius at gmail dot com

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The walkthrough data set is GEO accession GSE67959 , published in Nat Methods 2016 Jan;13(1):74-80. PMID: 26595209

Download instructions below.

Analysis workflow

Walkthrough with real data set

1. Design your capture oligonucleotide sequences with CapSequm webtool
2. Run CCseqBasic --onlyBlat to find the blacklisted homology regions for your capture locations
3. NG-captureC experiment(oligo synthesis, NG-captureC library generation, library sequencing)
4. Run CCseqBasic to your sequencing output fastq files (using the generated blacklist filtering file)

Below in detail

CapSequm

oligonucleotide designer

Walkthrough with real data set

CCseqBasic --onlyBlat

preparing homology filter for CaptureC data analysis

Walkthrough with real data set

CCseqBasic

CaptureC data analysis and QC

Walkthrough with real data set

CCseqBasic --snp

Investigating allelic skew

Walkthrough with real data set