STRT-N mouse library output files

<strong>Output files from STRT-N data analysis</strong> These files were obtained from a successful STRT-N mouse library using STRTN.sh, STRTN-UCSC-Allas.sh and STRTN-Seurat.sh. Details are below: <strong><code>OUTPUT</code>-QC.txt </strong><br> Quality check report for all samples. It is provided in <code>out</code> directory by STRTN.sh. Column Value <code>Barcode</code> Sample name. <code>OUTPUT</code> with numbers <code>Qualified_reads</code> Primary aligned read count <code>Total_reads</code> Read count without redundant (duplicate) reads <code>Redundancy</code> Qualified reads / Total reads <code>Mapped_reads</code> Mapped read count (Total reads without unmapped reads) <code>Mapped_rate</code> Mapped reads / Total reads <code>Spikein_reads</code> Read count mapped to ERCC spike-ins <code>Spikein-5end_reads</code> Read count mapped to the 5'-end 50 nt region of ERCC spike-ins <code>Spikein-5end_rate</code> Spikein-5end reads / Spikein reads <code>Coding_reads</code> Read count aligned within any exon or the 500 bp upstream of coding genes <code>Coding-5end_reads</code> Read count aligned the 5′-UTR or 500 bp upstream of coding genes <code>Coding-5end_rate</code> Coding-5end reads / Coding reads <strong><code>OUTPUT</code>-QC-plots.pdf</strong><br> Quality check report by boxplots. <code>Mapped_reads</code>, <code>Mapped_rate</code>, <code>Spikein_reads</code>, <code>Mapped / Spikein</code>, <code>Spikein-5end_rate</code>, and <code>Coding-5end_rate</code> are shown for all samples. Barcode numbers of outlier samples are marked with red characters. It is provided in <code>out</code> directory by STRTN.sh.<br> Please consider these outlier samples for the further downstream analysis. <strong><code>OUTPUT</code>_byGene-counts.txt</strong><br> Read count table output from. It is provided in <code>out</code> directory by STRTN.sh.<br> featureCounts. https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf <strong><code>OUTPUT</code>_byGene-counts.txt.summary</strong><br> Filtering summary from. It is provided in <code>out</code> directory by STRTN.sh. <br> featureCounts. https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf <strong>Output_bam</strong><br> Resulting BAM files including unmapped, non-primary aligned, and duplicated (marked) reads. Files are provided in <code>out</code> directory by STRTN.sh. <strong>Output_bai</strong><br> Index files (.bai) of the resulting BAM files in the <code>Output_bam</code> directory. Files are provided in <code>out</code> directory by STRTN.sh. <strong><code>OUTPUT</code>.output.bam</strong><br> BAM files containing reads except for duplicate and non-primary reads. Files are provided in the working directory by STRTN.sh. <strong><code>OUTPUT</code>.minus.bw</strong> and <strong><code>OUTPUT</code>.plus.bw</strong><br> BigWig files for each strands of each sample. Files are provided in the working directory by STRTN.sh. <strong>coding_5end.bb</strong><br> BigBed file for coding-5'end annotation file. It is provided in the working directory by STRTN.sh <strong>hub.txt</strong><br> Parameters for each tracks. It is provided in the working directory by STRTN-UCSC-Allas.sh. <strong>Link of hub.txt file</strong><br> Provided by STRTN-UCSC-Allas.sh. <strong><code>OUTPUT</code>-QC-BeeswarmPlots.pdf</strong><br> Visualization quality check values for each developmental stage using BeeswarmPlots. It is provided in <code>out</code> directory by STRTN-Seurat.sh. <strong>Rplots.pdf</strong><br> Elbow, JackStraw, PCA, UMAP and violin plots. It is provided in <code>out</code> directory by STRTN-Seurat.sh. <strong>ExtractIlluminaBarcodes_Metrics</strong><br> Metrics file produced by the Picard ExtractIlluminaBarcodes program. The number of matches/mismatches between the barcode reads and the actual barcodes is shown per lane. https://gatk.broadinstitute.org/hc/en-us/articles/360037426491-ExtractIlluminaBarcodes-Picard- <strong>HISAT2_Metrics</strong><br> Alignment summary of samples from each lane produced by the HISAT2 program. https://daehwankimlab.github.io/hisat2/manual/ <strong>MarkDuplicates_Metrics</strong><br> Metrics file indicating the numbers of duplicates produced by the Picard MarkDuplicates program. https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- <strong><code>OUTPUT_</code>MultiQC_report.html </strong><br> For each sample, fastq files from the output BAM files are generated by fastq-fastQC.sh in the <code>fastq</code> directory. These fastq files (without duplicated reads) can be submitted to public sequence databases. FastQC files are also generated for each fastq file in the <code>fastqc</code> directory. Based on the FastQC results, MultiQC report (<strong>MultiQC_report.html</strong>) is generated. <strong><code>OUTPUT_</code>byTFE-counts_annotation.txt</strong><br> Read count table output from featureCounts with genomic annotations, produced by STRTN-TFE.sh. <strong><code>OUTPUT_</code>peaks.bed</strong><br> Peak position information of TFEs, produced by STRTN-TFE.sh. <strong><code>OUTPUT_</code>annotation</strong><br> Annotation of TFEs, produced by STRTN-TFE.sh.