Date post: | 16-Apr-2017 |
Category: |
Science |
Upload: | fritz-sedlazeck |
View: | 230 times |
Download: | 2 times |
SVs Hackathon group
10x genomics● Library preparation system for
illumina reads
● WGS, single cell, Exon Seq, RNA-Seq,
● Assigns barcodes to pairs that belong to the same molecule
● Software: ○ Longranger (mapping + SNPs)○ Supernova (Assembly)
● Rising star in the field -> More (specialized) software will be required
1. Topsorter:Graph based assessment of SVs using 10x genomics
1.1 Get data (GIAB + NA12878) (done)
1.2 Call SVs (done)
1.3 Retrieve barcode information (done)
1.4 Construct a weighted DAG w/ chr + SVs (done)
1.5 Update the weights with barcode density and additional information (in progress)
1.6 Use topological sorting to find the longest graph and see if SVs exists (done)
1.7 F1000 Paper (in progress)
Chromosome 20
DEL REFREF
DUP REFREF
DUP_COPY
INV (S,E)
REFREF
INV_FLIP(E,S)
238 377
22
Construct a DAG with SV orientation
Update the graph weights of barcode densities
Find the longest path in a graph
Mostly likely haplotype for each chromosome
2. GLRSim/Mr. Fantastic 10x genomics read simulator
2.1 Agree on list of parameters (done)
2.2 Obtain real data (13 data sets) (done)
2.3 Obtain further insights based on real data (done)
2.3 Construct the pipeline (done)
2.4 Compare to real data (todo)
2.5 Write up as Bioinformatics applications note (in progress)
3. DangerTrackDifficult to assess regions
3.1 Collect SVs (1k + GIAB ) (done)
3.2 Collect repetitive regions (done)
3.3 Collect GC levels (done)
3.4 Collect breakpoint positions with e.g. 5kb (done)
3.5 Test pipeline for updates to GRCh38 (in progress)
3.6 Comparison to known problematic regions (done)
3.7 F1000 paper (in progress)
● 5kb region
● Normalized breakpoints
● 1-mappability
● GC content
● Combined score is the average of tracks.
Example on hg19:
Chr3:
Chr5:NCBI region list
Encode blacklist