Package: trackplot
trackplotTutorialswhat is trackplottrackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.Features of trackplotSupport various file formats as inputSupport strand-aware coverage plotVisualize coverage by heatmap, including HiC diagramVisualize protein domain based the given gene idDemultiplex the single-cell RNA/ATAC-seq which used cell barcode into cell populationSupport visualizing individual full-length reads in read-by-read styleSupport visualize circRNA sequencing dataInputtrackplot supports almost NGS data format, includingBAMBedDepth file generated bysamtools depthbigBed [pyBigWigoptional]bigWig [pyBigWigoptional]naive Hi-C format [hicmatrixoptional]OutputThe output will be a pdf and other image file formats which satisfy the requirement of the major journals,
and each track on output corresponds these datasets from config file.UsageTrackplot is based onPython3(python_requires='>=3.8'),
and we have simplified the installation process on the main page.
For a more comprehensive installation guide, please refer tothis link.For impatientpipinstalltrackplot
trackplot--help# or using trackplot by condacondacreate-ntrackplot-cbioconda-cconda-forgetrackplot
condaactivatetrackplot
trackplot--helpNotesFor users onMicrosoft Windows,Mac (Apple Silicon),
andother ARM platforms,
please note that Trackplot may not be installable via PyPI or Conda due to compatibility issues with pysam,
pybigwig, and hicmatrix libraries on these platforms.
As an alternative, we recommend using the Docker image for installation.If you encounter asegment faulterror during multiple processing,
you may want to consider using the Docker image or running the command with the-p 1flag.If you encounter the messagePlease install pyBigWig and hicmatrix,
you can refer to the official documentation forpyBigWigandhicmatrixto fulfill their requirements and resolve the issue.Using trackplot by a command line (click me)install from PyPiBefore running this command line, please check python (>=3.8) was installed.pipinstalltrackplot# __Note:__ We noticed some pypi mirrors are not syncing some packages we depend on,# therefore please try another pypi mirror once you encounter# `No local packages or working download links found for xxx`AppImage(Linux/WSL x86_64 platform only)For a binary version of the tool and more comprehensive information, please visitthis link.# example with version v0.3.5, please using your interested version according to your needsexportVERSION=0.3.5
chmod+xtrackplot-${VERSION}-x86_64.AppImage
./trackplot-${VERSION}-x86_64.AppImage--helpusing docker imagedockerpullygidtu/trackplot
dockerrun--rmygidtu/trackplot--helpinstall from bioconda# install trackplot into the default conda envcondainstall-cbioconda-cconda-forgetrackplot# or install trackplot into an isolated environmentscondacreate-ntrackplot-cbioconda-cconda-forgetrackplot# activate the trackplot environment and execute the command line toolcondaactivatetrackplot
trackplot--helpUsing trackplot by a local webserver (click me)AppImage(Linux/WSL x86_64 only)# example with version v0.3.3, please using your interested version according to your needsexportVERSION=0.3.3
gunziptrackplot-${VERSION}-x86_64.AppImage
chmod+xtrackplot-${VERSION}-x86_64.AppImage
./trackplot-${VERSION}-x86_64.AppImage--help# startup webserver./trackplot-${VERSION}-x86_64.AppImage--start-server--host0.0.0.0--port5000--plots./plotsNote:the--plotswere required while using appimagesRunning using command linetrackplot--start-server--host0.0.0.0--port5000--plots./plotsRunning using docker imagedockerpullygidtu/trackplot# Deploy the serverdockerrun--nametrackplot\--rm-v$PWD/example:/data-v$PWD/plots/:/plots-p5000:5000ygidtu/trackplot\--start-server\--host0.0.0.0\--data/data\--plots/plots-p: public and private port for the server, default:5000(public):5000(private)-v,--volume: mount the working directory to docker container, for example, the$PWD/datacould replace by the path to your directory contains all necessary data--user: prevent docker read and write file using root privilegesExampleTheexamplefolder is downloaded fromhere.And a more detailed tutorial could be found athere.# example of basic plot typestrackplot\-echr1:1270656-1284730:+\-rexample/example.sorted.gtf.gz\--intervalexample/interval_list.tsv\--densityexample/density_list.tsv\--show-junction-num\--igvexample/igv.tsv\--heatmapexample/heatmap_list.tsv\--focus1272656-1272656:1275656-1277656\--stroke1275656-1277656:1277856-1278656@blue\--sites1271656,1271656,1272656\--lineexample/line_list.tsv\-oexample.png\--dpi300\--width10\--height1\--barcodeexample/barcode_list.tsv\--domain--remove-duplicate-umi\--normalize-formatcpm\--annotation-scale.3\-p4if trackplot was installed by docker, here is the cmd## The absolute path is required in Docker env.cat$PWD/example/interval_list.tsv|grep-v'^#'|whilereadline;doecho$PWD/${line};done>$PWD/example/interval_list.abspath.tsv
cat$PWD/example/density_list.tsv|grep-v'^#'|whilereadline;doecho$PWD/${line};done>$PWD/example/density_list.abspath.tsv
cat$PWD/example/igv.tsv|grep-v'^#'|whilereadline;doecho$PWD/${line};done>$PWD/example/igv.abspath.tsv
cat$PWD/example/heatmap_list.tsv|grep-v'^#'|whilereadline;doecho$PWD/${line};done>$PWD/example/heatmap_list.abspath.tsv

dockerrun-v$PWD:$PWD-w$PWD--rmygidtu/trackplot\-echr1:1270656-1284730:+\-r$PWD/example/example.sorted.gtf.gz\--interval$PWD/example/interval_list.tsv\--density$PWD/example/density_list.tsv\--show-junction-num\--igv$PWD/example/igv.tsv\--heatmap$PWD/example/heatmap_list.tsv\--focus1272656-1272656:1275656-1277656\--stroke1275656-1277656:1277856-1278656@blue\--sites1271656,1271656,1272656\--line$PWD/example/line_list.tsv\-oexample.png\--dpi300\--width10\--height1\--barcode$PWD/example/barcode_list.tsv\--domain--remove-duplicate-umi\--normalize-formatcpm\--annotation-scale.3\-p4here is theoutput file.QuestionsVisitissuesor
contactYiming ZhangorRan ZhouCitationIf you use the tool in your publication, please cite byZhang Y, Zhou R, Liu L, et al. Trackplot: A flexible toolkit for combinatorial analysis of genomic data[J]. PLoS computational biology, 2023, 19(9): e1011477.