Plot read coverage for a GRanges objectYue Li
D) Transcript percentage for four of the five DUSP13 annotated transcripts with high read coverage in the GTEx v8. Extended Data Fig. 13 Differential expression analysis between PTBP1-KD and control samples. A) Volcano plot from differential gene expression between control and samples with PTBP1...
'window.size','average.coverage')head(fwd.df)rev.df<-read.delim('rev.depth.txt',sep='\t',header=FALSE)names(rev.df)<-c('chr','start','end','read.counts','base.number','window.size','average.coverage
istanbul - Yet another JS code coverage tool. blanket - A simple code coverage library for JavaScript. Designed to be easy to install and use, for both browser and nodejs. JSCover - JSCover is a tool that measures code coverage for JavaScript programs....
scReadSim’s synthetic scATAC-seq data mimic the real sci-ATAC-seq dataset23in terms of the cell-type-specific read coverage (a), the fragment-size distribution (b), the substitution error rate per base within a read (c), and the peaks called by MACS3 at the pseudo-bulk level (d; ...
Using something like that, we can plot the distribution from the entire genome. Below we show this for samples with ~60X coverage: We can also view the Y chromosome to verify that males and females track separately. Below, we that see female samples cluster along the axes while male sample...
stephenturner/solarplot seandavi/sars2pack tanghaibao/allhic freeseek/gwaspipeline tseemann/homebrew-bioinformatics-linux brentp/bsub statgen/fastQValidator broadinstitute/SignatureAnalyzer-GPU biowdl/tasks jodyphelan/TBProfiler brentp/gsort brentp/geneimpacts brentp/poverlap broadinstitute/long-read-pipeli...
Data for coverage plots were generated using SAMtools depth with the -a and -Q 0 flags; a custom script then calculated the average coverage in 1 kbp nonoverlapping windows. Plots were generated using average coverage in karyoploteR.30 Southern blot of family 04 Southern blot was performed usin...
5.2 Assembly graph analysis of a synthetic low-coverage datasetThis section gives an introductory overview of the analyses that our method performs on the T.roseus simple synthetic dataset described above. Canu produced three contigs of total length 4.7 Mbp. A ≈ 500 kb region is missing ...
five disks in each direction provide coverage at larger absolute values of pseudorapidity. With the current configuration, the material budget they contributed is less than 5%\(X_0\). This geometry was implemented in GEANT4 and studied within the full Monte-Carlo framework for detector simulation...