Scapture

Author: q | 2025-04-25

sCapture Download. sCapture (โปรแกรม sCapture ถ่ายรูปสินค้า เพื่อ สร้างบาร์โค้ด): สำหรับโปรแกรมที่มีชื่อว่า โปรแกรม sCapture มันเป็นโปรแกรมที่ใช้สำหรับการถ่ายรูปภาพ sCapture (โปรแกรม sCapture ถ่ายรูปสินค้า เพื่อ สร้างบาร์โค้ด) 1.0. ดาวน์โหลดโปรแกรม sCapture เครื่องมือถ่ายภาพสินค้า รหัสบาร์โค้ดที่เตรียมจะ

SCAPTURE/scapture at main YangLab/SCAPTURE

SCAPTUREDescription:SCAPRUTE pipeline. A deep learning-embedded pipeline that captures polyadenylation information from 3 prime tag-based RNA-seq of single cellsInstallation:Require Bedtools v2.26.0Require featureCounts ≥ v1.6.2Create conda env from SCAPTURE yaml file: conda env create -f SCAPTURE_env.yamlDownload and unzip package from Github, then add "+x" to scripts to make it executable. unzip SCAPTURE-main.zip cd SCAPTURE-main/ chmod +x scapture scapture_annotation scapture_callpeak scapture_evaluate scapture_mergesample scapture_quantExport path of SCAPTURE suite to environment SCAPTURE="/Your_Path/SCAPTURE-main"Add SCAPTURE to ./bashrc file of your environment.> ~/.bashrc"> echo "export ${SCAPTURE}:\$PATH" >> ~/.bashrcOr manually export to environment variable before running SCAPTURE export PATH=${SCAPTURE}:$PATHTest whether SCAPTURE could be found which scapture "/Your_Path/SCAPTURE-main/scapture"Activate SCAPTURE_env environment before running SCAPTURE conda activate SCAPTURE_envUsage: [options] -h/---help -- help information">scapture -m [options] -h/---help -- help informationModule: annotationOptions:-o -- prefix of the output files-g -- genome .fa file--gtf -- gene annotation file (GTF format, recomannd GENOCODE annotation with "gene_name" and "gene_type" tags)--cs -- chromosom size file--extend -- extended dowstream distance of 3 prime gene annotation to call peaks (bp, default: 2000)-h/---help -- help informationModule: PAScallOptions:-a -- prefix of output annotation files in "annotation" module-o -- prefix of output file-b -- Cell Ranger aligned BAM file-g -- genome .fa file-p -- number of cores-l -- read length of sequenceing cDNA in scRNA-seq-w -- width of poly(A) peaks (default: 400)--species -- species for DeepPASS model ('human', 'mouse')--overlap -- overlapped ratio of exonic peaks to merge (default: 0.5)--polyaDB -- poly(A) site database bed6 file (optional)-h/---help -- help informationModule: PASmergeOptions:-o -- prefix of output file--peak -- list of evaluated peak files to merge (one sample per line, split by tab, 1st col: "Sample_name", 2cd col: "PathofEvaluatedPeakFile" )--path -- path of scapture suite (ignore if scapture in PATH)--rawpeak -- raw peak files to merge (Restricted by --peak)-h/---help -- help informationModule: PASquantOptions:-o -- output prefix-p -- number of threads-b -- Cell Ranger aligned BAM file--pas --

SCAPTURE/scapture at main YangLab/SCAPTURE - GitHub

PASs peaks file to quantify--celllist -- cell barcode file as white list(one barcode per line), or use "--celllist FromBAM" to used all cell barcode from input BAM (for unfiltered BAM, it might take lots of time).--celltype -- cell type annotation file (tab split, 1st col: "cell_barcode", 2cd col: "cell_type" ).--bw -- generate bigwiggle file for each cell type in --celltype option (true, false, default: false)-h/---help -- help informationVersion: 1.0 2021/01/25Author: Guo-Wei Li Email: [email protected] protocolWe use six human PBMC scRNA-seq datasets from 10x Genomics to show step-by-step protocol of SCAPTURE. All files used/generated by this example could be found at shared Google Drive.File preparationMake sure that featureCounts and SCAPTURE are available in your PATH. User can manually add software path to PATH, like: export PATH=/home/software/SCAPTURE-main:$PATH export PATH=/home/software/subread-1.6.2-Linux-x86_64/bin:$PATHPrepare gene annotation and genome file. In this example, we use annotation from GENCODE hg38. SCAPTURE supports references given by users for specific study. Currently, we take GENCODE GTF file as gene annotation. GENCODE GTF annotation contains "gene_name" and "gene_type" in the 8th column field, and SCAPTURE utilizes the information to annotate PAS from genes. However, it is not necessary for the future (we are working on it). gencode.v34.annotation.gtf hg38.chromsize genome.fa genome.fa.faiIf poly(A) databases file (BED format, optional) is given, SCAPTURE will annotate PAS with database information and select relatively high confident PAS during merging different samples (in SCAPTURE PASmerge step). Combined PolyADB3, PolyA-Seq, PolyASite and GENCODE poly(A) databases file: human hg38 (SupTab_KnownPASs_fourDBs.txt), mouse mm10 (mm10.SupTab_KnownPASs_fourDBs.txt). SupTab_KnownPASs_fourDBs.txtFor running demo, we extracted reads in chr1:1-10000000 region from aligned BAM file of PBMCs in out study. And the white cell barcode list in each sample (generated by Cell Ranger count or given by the user). All used files could be found at here. ls ./PBMC* PBMC10k.test.bam PBMC8k.test.bam PBMC6k.test.bam PBMC5k.test.bam PBMC4k.test.bam PBMC3k.test.bam PBMC10k.test.bam.bai PBMC8k.test.bam.bai PBMC6k.test.bam.bai PBMC5k.test.bam.bai PBMC4k.test.bam.bai

Scapture-official/Scapture-Client: SCAPTURE-Client - GitHub

Knowing keyboard alternatives is essential to boost productivity on a Mac system. This guide on VLC keyboard shortcuts for Mac provides quick and efficient ways to adjust volume, play and pause media, and take screenshots. By learning these alternate approaches, you can save time and have a smoother experience while using VLC. So, keep reading to learn more.VLC media player is a popular media player for Mac that can play various video and audio formats with a user-friendly interface. By using these alternatives, users can boost their productivity and perform tasks quickly without the need for a mouse. To learn about it more and improve your experience with VLC, refer to the table below.VLC Shortcut MacFunctionCommand+FWith this enter Fullscreen mode.EscIt exits the Full Screen mode.SpacebarWith this key pause or play the video.STurn On/Off Subtitles with it.Command+Ctrl+Left/Right (short), Command+Option+Left/Right (Medium), Command+Shift+Left/Right (Long)Jump Forward/Backward with this keyboard shortcuts. In this short means 3 seconds, medium means 10 seconds and long means 1 minute jump.Command+Up/Down arrowWith this control the volume.Command+Option+DownPress and hold these keys to Mute the volume.Command+OOpen File with this shortcut.AIt changes the Aspect ratio.Decrease “H”, Increase “J”This controls the subtitle delay.Decrease “F”, Increase “G”With this control the audio delay.EIt makes video move frame by frame.Command+HTo hide the controls, use this shortcut.Command+PUse this shortcut to access the preferences.Command+BThis controls the bookmarks.Open “Command+L”, Save “Command+Y”To open and save the playlist.Next “Command+Right Arrow Key”, Previous “Command+Left Arrow Key”With this play the next or previous track.ZChange the zoom mode with this VLC keyboard shortcut.Command+EGet hold of effects and filters menu.TTo view the playback time use this.Increase “Command and+”, Decrease “Command+-”Use this to increase and decrease the playback speed.Shift+SCapture screenshot with this keyboard shortcut.Command + DTo launch the Disc menu.Ctrl + mWith this navigate to DVD menu.Ctrl + pYou can choose the earlier DVD title using this shortcut keys.Ctrl + nTo choose the next DVD title.Cmd + qQuit using this shortcut.lTo cycle audio track.Opt + oWith this, escalate the scale factor.Opt + Shift + oReduces the scale factor.Cmd + Shift + rTo record, use this shortcut.Opt + iFrom the top of the video crop one pixel.Opt. sCapture Download. sCapture (โปรแกรม sCapture ถ่ายรูปสินค้า เพื่อ สร้างบาร์โค้ด): สำหรับโปรแกรมที่มีชื่อว่า โปรแกรม sCapture มันเป็นโปรแกรมที่ใช้สำหรับการถ่ายรูปภาพ

sCapture แหล่งดาวน์โหลด sCapture ฟรี

PBMC3k.test.bam.bai PBMC10k.celllist PBMC8k.celllist PBMC6k.celllist PBMC5k.celllist PBMC4k.celllist PBMC3k.celllistRun scapture annotation moduleIn this step, SCAPTURE will generate annotation files for downstream analysis. If your study includes multiple samples, we recommend using the same annotation files in this step to analyze all samples. annotation.log">scapture -m annotation -o SCAPTURE_annotation -g genome.fa --gtf hg38.gtf --cs hg38.chromsize --extend 2000 &> annotation.logOutput files in this step:ls SCAPTURE_annotation*SCAPTURE_annotation.chromsize SCAPTURE_annotation.genetype.bed SCAPTURE_annotation.genetype.gtfSCAPTURE_annotation.element.txt SCAPTURE_annotation.genetype.extended.bed SCAPTURE_annotation.genetype.txtRun scapture PAScall moduleSCAPTURE takes aligned BAM files and above annotation files as input to call peaks. The PAScall module contains several steps:(1) perform transcript level peak calling and filtering(2) assign peak to APA-transcript (see detail in our paper)(3) evaluate peak with DeepPASS prediction (automatically run) and poly(A) database annotation (optional) PBMC3k.PAScall.logscapture -m PAScall -a SCAPTURE_annotation -g genome.fa -b PBMC4k.test.bam -l 98 -o PBMC4k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC4k.PAScall.logscapture -m PAScall -a SCAPTURE_annotation -g genome.fa -b PBMC5k.test.bam -l 91 -o PBMC5k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC5k.PAScall.logscapture -m PAScall -a SCAPTURE_annotation -g genome.fa -b PBMC6k.test.bam -l 98 -o PBMC6k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC6k.PAScall.logscapture -m PAScall -a SCAPTURE_annotation -g genome.fa -b PBMC8k.test.bam -l 98 -o PBMC8k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC8k.PAScall.logscapture -m PAScall -a SCAPTURE_annotation -g genome.fa -b PBMC10k.test.bam -l 91 -o PBMC10k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC10k.PAScall.log">scapture -m PAScall -a SCAPTURE_annotation -g genome.fa -b PBMC3k.test.bam -l 98 -o PBMC3k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC3k.PAScall.logscapture -m PAScall -a SCAPTURE_annotation -g genome.fa -b PBMC4k.test.bam -l 98 -o PBMC4k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC4k.PAScall.logscapture -m PAScall -a SCAPTURE_annotation -g genome.fa -b PBMC5k.test.bam -l 91 -o PBMC5k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC5k.PAScall.logscapture -m PAScall -a SCAPTURE_annotation -g genome.fa -b PBMC6k.test.bam -l 98 -o PBMC6k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC6k.PAScall.logscapture -m PAScall -a SCAPTURE_annotation -g

Scapture-official/Scapture-Client: ⚽SCAPTURE-Client - GitHub

Genome.fa -b PBMC8k.test.bam -l 98 -o PBMC8k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC8k.PAScall.logscapture -m PAScall -a SCAPTURE_annotation -g genome.fa -b PBMC10k.test.bam -l 91 -o PBMC10k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC10k.PAScall.logOutput files in this step:#for the PBMC3k sample, we got:PBMC3k.exonic.peaks.bed # filtered exonic peaksPBMC3k.exonic.peaks.annotated.bed # assigned exonic peaksPBMC3k.exonic.peaks.evaluated.bed # evaluated exonic peaksPBMC3k.intronic.peaks.bed # filtered intronic peaksPBMC3k.intronic.peaks.annotated.bed # assigned intronic peaksPBMC3k.intronic.peaks.evaluated.bed # evaluated intronic peaksPBMC3k.3primeExtended.peaks.annotated.bed # assigned peaks in dowstream region beyond 3' end of genesPBMC3k.3primeExtended.peaks.evaluated.bed # evaluated peaks in dowstream region beyond 3' end of genesThe output poly(A) site file was in widely-used BED format see.Briefly,the 1-12 columns represent the spliced peak region of PAS. seeSpecifically, for "evaluated.bed",the 13th column is "number of refernce poly(A) sites supporting the PAS."the 14th column is "DeepPASS prediction of the PAS."the 15th column is "±100 nt sequence around the cleavage site of PAS."Run scapture PASmerge moduleIf your study includes multiple samples, SCAPTURE can merge the peak result from all samples, and create a combined peak reference file for downstream analysis. PBMC_ALL.exonic.peaklistfor i in 3 4 5 6 8 10; do echo -e PBMC${i}k"\t"PBMC${i}k.intronic.peaks.evaluated.bed; done > PBMC_ALL.intronic.peaklistfor i in 3 4 5 6 8 10; do echo -e PBMC${i}k"\t"PBMC${i}k.3primeExtended.peaks.evaluated.bed; done > PBMC_ALL.3primeExtended.peaklist#run the PASmerge modulescapture -m PASmerge -o PBMC_ALL.exonic --peak PBMC_ALL.exonic.peaklist &> PBMC_ALL.PASmerge.exonic.logscapture -m PASmerge -o PBMC_ALL.intronic --peak PBMC_ALL.intronic.peaklist &> PBMC_ALL.PASmerge.intronic.logscapture -m PASmerge -o PBMC_ALL.3primeExtended --peak PBMC_ALL.3primeExtended.peaklist &> PBMC_ALL.PASmerge.3primeExtended.log">#create table with sample name and sample peak file path:for i in 3 4 5 6 8 10; do echo -e PBMC${i}k"\t"PBMC${i}k.exonic.peaks.evaluated.bed; done > PBMC_ALL.exonic.peaklistfor i in 3 4 5 6 8 10; do echo -e PBMC${i}k"\t"PBMC${i}k.intronic.peaks.evaluated.bed; done > PBMC_ALL.intronic.peaklistfor i in 3 4 5 6 8 10; do echo -e PBMC${i}k"\t"PBMC${i}k.3primeExtended.peaks.evaluated.bed; done > PBMC_ALL.3primeExtended.peaklist#run the PASmerge modulescapture -m PASmerge -o PBMC_ALL.exonic --peak PBMC_ALL.exonic.peaklist &> PBMC_ALL.PASmerge.exonic.logscapture -m PASmerge -o PBMC_ALL.intronic --peak PBMC_ALL.intronic.peaklist &>

sCapture (โปรแกรม sCapture ถ่ายรูปสินค้า เพื่อ สร้างบาร์โค้ด)

PBMC_ALL.PASmerge.intronic.logscapture -m PASmerge -o PBMC_ALL.3primeExtended --peak PBMC_ALL.3primeExtended.peaklist &> PBMC_ALL.PASmerge.3primeExtended.logOutput files in this step:# Integrated peaksPBMC_ALL.exonic.Integrated.bedPBMC_ALL.intronic.Integrated.bedPBMC_ALL.3primeExtended.Integrated.bed# Integrated peaks with original record of all samplesPBMC_ALL.exonic.IntegratedSamples.bedPBMC_ALL.intronic.IntegratedSamples.bedPBMC_ALL.3primeExtended.IntegratedSamples.bedCombined peaks are written in files with "Integrated.bed" BED format see,the 1-12 columns represent the spliced peak region of PAS see.the 13th column is "number of refernce poly(A) sites supporting the PAS."the 14th column is "DeepPASS prediction of the PAS."the 15th column is "±100 nt sequence around the cleavage site of PAS."Specifically, for "IntegratedSamples.bed" (ignored, not used in downstream analysis),the 16th column is the index id during peak combination.the 17th column the number of peaks with the same index id.Run scapture PASquant moduleFor PAS quantifying at single-cell level expression, users can chose different subset of PASs for their goals. In our paper, we recomanded select the high-cofident PASs with positive prediction and konwn sites overlapped. 0 | $F[13] eq "positive";' PBMC_ALL.exonic.Integrated.bed PBMC_ALL.intronic.Integrated.bed > PBMC_ALL.PASquant.bed# 2. Select PASs with positive prediction (no konwn sites filter)perl -alne '$,="\t";print @F[0..11] if $F[13] eq "positive";' PBMC_ALL.exonic.Integrated.bed PBMC_ALL.intronic.Integrated.bed > PBMC_ALL.PASquant.bed# 3. Select all raw PASsperl -alne '$,="\t";print @F[0..11];' PBMC_ALL.exonic.Integrated.bed PBMC_ALL.intronic.Integrated.bed > PBMC_ALL.PASquant.bed"># 1. Select PASs with positive prediction and konwn sites overlapped (recomanded)perl -alne '$,="\t";print @F[0..11] if $F[12] > 0 | $F[13] eq "positive";' PBMC_ALL.exonic.Integrated.bed PBMC_ALL.intronic.Integrated.bed > PBMC_ALL.PASquant.bed# 2. Select PASs with positive prediction (no konwn sites filter)perl -alne '$,="\t";print @F[0..11] if $F[13] eq "positive";' PBMC_ALL.exonic.Integrated.bed PBMC_ALL.intronic.Integrated.bed > PBMC_ALL.PASquant.bed# 3. Select all raw PASsperl -alne '$,="\t";print @F[0..11];' PBMC_ALL.exonic.Integrated.bed PBMC_ALL.intronic.Integrated.bed > PBMC_ALL.PASquant.bedQuantify high-confidence PASs in six PBMC samples: PBMC3k.PASquant.logscapture -m PASquant -b PBMC4k.test.bam --celllist PBMC4k.celllist --pas PBMC_ALL.PASquant.bed -o PBMC4k.PASquant &> PBMC4k.PASquant.logscapture -m PASquant -b PBMC5k.test.bam --celllist PBMC5k.celllist --pas PBMC_ALL.PASquant.bed -o PBMC5k.PASquant &> PBMC5k.PASquant.logscapture -m PASquant -b PBMC6k.test.bam --celllist PBMC6k.celllist --pas PBMC_ALL.PASquant.bed -o PBMC6k.PASquant &> PBMC6k.PASquant.logscapture -m PASquant -b PBMC8k.test.bam --celllist PBMC8k.celllist --pas PBMC_ALL.PASquant.bed -o PBMC8k.PASquant &> PBMC8k.PASquant.logscapture -m PASquant -b PBMC10k.test.bam --celllist PBMC10k.celllist --pas. sCapture Download. sCapture (โปรแกรม sCapture ถ่ายรูปสินค้า เพื่อ สร้างบาร์โค้ด): สำหรับโปรแกรมที่มีชื่อว่า โปรแกรม sCapture มันเป็นโปรแกรมที่ใช้สำหรับการถ่ายรูปภาพ sCapture (โปรแกรม sCapture ถ่ายรูปสินค้า เพื่อ สร้างบาร์โค้ด) 1.0. ดาวน์โหลดโปรแกรม sCapture เครื่องมือถ่ายภาพสินค้า รหัสบาร์โค้ดที่เตรียมจะ