STRT-N mouse library output files

Output files from STRT-N pipeline These files were obtained from a successful STRT-N mouse library using STRT-N pipelines. Details are below: OUTPUT-QC.txt Quality check report for all samples. Column Value Barcode Sample name. OUTPUT with numbers Qualified_reads Primary aligned read count Total_reads Read count without redundant (duplicate) reads Redundancy Qualified reads / Total reads Mapped_reads Mapped read count (Total reads without unmapped reads) Mapped_rate Mapped reads / Total reads Spikein_reads Read count mapped to ERCC spike-ins Spikein-5end_reads Read count mapped to the 5'-end 50 nt region of ERCC spike-ins Spikein-5end_rate Spikein-5end reads / Spikein reads Coding_reads Read count aligned within any exon or the 500 bp upstream of coding genes Coding-5end_reads Read count aligned the 5′-UTR or 500 bp upstream of coding genes Coding-5end_rate Coding-5end reads / Coding reads OUTPUT-QC-plots.pdf Quality check report by boxplots. Mapped_reads, Mapped_rate, Spikein_reads, Mapped / Spikein, Spikein-5end_rate, and Coding-5end_rate are shown for all samples. Barcode numbers of outlier samples are marked with red characters. Please consider these outlier samples for the further downstream analysis. OUTPUT_byGene-counts.txt Read count table output from featureCounts. https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf OUTPUT_byGene-counts.txt.summary Filtering summary from featureCounts. https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf Output_bam Resulting BAM files including unmapped, non-primary aligned, and duplicated (marked) reads. Output_bai Index files (.bai) of the resulting BAM files in the Output_bam directory. OUTPUT.output.bam BAM files containing reads except for duplicate and non-primary reads. OUTPUT.minus.bw and OUTPUT.plus.bw BigWig files for each strands of each sample. coding_5end.bb BigBed file for coding-5'end annotation file. hub.txt Parameters for each tracks. Link of hub.txt file OUTPUT-QC-BeeswarmPlots.pdf Visualization quality check values for each developmental stage using BeeswarmPlots. Rplots.pdf Elbow, JackStraw, PCA, UMAP and violin plots