STRT-N mouse library output files

<p><strong>Output files from STRT-N data analysis</strong></p> <p>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:</p> <ul> <li> <p><strong><code>OUTPUT</code>-QC.txt&nbsp;</strong><br> Quality check report for all samples.&nbsp;It is provided in&nbsp;<code>out</code>&nbsp;directory by&nbsp;STRTN.sh.</p> <table> <thead> <tr> <th>Column</th> <th>Value</th> </tr> </thead> <tbody> <tr> <td><code>Barcode</code></td> <td>Sample name.&nbsp;<code>OUTPUT</code>&nbsp;with numbers</td> </tr> <tr> <td><code>Qualified_reads</code></td> <td>Primary aligned read count</td> </tr> <tr> <td><code>Total_reads</code></td> <td>Read count without redundant (duplicate) reads</td> </tr> <tr> <td><code>Redundancy</code></td> <td>Qualified reads / Total reads</td> </tr> <tr> <td><code>Mapped_reads</code></td> <td>Mapped read count (Total reads without unmapped reads)</td> </tr> <tr> <td><code>Mapped_rate</code></td> <td>Mapped reads / Total reads</td> </tr> <tr> <td><code>Spikein_reads</code></td> <td>Read count mapped to ERCC spike-ins</td> </tr> <tr> <td><code>Spikein-5end_reads</code></td> <td>Read count mapped to the 5&#39;-end 50 nt region of ERCC spike-ins</td> </tr> <tr> <td><code>Spikein-5end_rate</code></td> <td>Spikein-5end reads / Spikein reads</td> </tr> <tr> <td><code>Coding_reads</code></td> <td>Read count aligned within any exon or the 500 bp upstream of coding genes</td> </tr> <tr> <td><code>Coding-5end_reads</code></td> <td>Read count aligned the 5&prime;-UTR or 500 bp upstream of coding genes</td> </tr> <tr> <td><code>Coding-5end_rate</code></td> <td>Coding-5end reads / Coding reads</td> </tr> </tbody> </table> </li> <li> <p><strong><code>OUTPUT</code>-QC-plots.pdf</strong><br> Quality check report by boxplots.&nbsp;<code>Mapped_reads</code>,&nbsp;<code>Mapped_rate</code>,&nbsp;<code>Spikein_reads</code>,&nbsp;<code>Mapped / Spikein</code>,&nbsp;<code>Spikein-5end_rate</code>, and&nbsp;<code>Coding-5end_rate</code>&nbsp;are shown for all samples. Barcode numbers of outlier samples are marked with red characters.&nbsp;It is provided in&nbsp;<code>out</code>&nbsp;directory&nbsp;by&nbsp;STRTN.sh.<br> Please consider these outlier samples for the further downstream analysis.</p> </li> <li> <p><strong><code>OUTPUT</code>_byGene-counts.txt</strong><br> Read count table output from.&nbsp;It is provided in&nbsp;<code>out</code>&nbsp;directory by&nbsp;STRTN.sh.<br> featureCounts.&nbsp;<a href="https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf">https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf</a></p> </li> <li> <p><strong><code>OUTPUT</code>_byGene-counts.txt.summary</strong><br> Filtering summary from.&nbsp;It is provided in&nbsp;<code>out</code>&nbsp;directory by&nbsp;STRTN.sh.&nbsp;<br> featureCounts.&nbsp;<a href="https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf">https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf</a></p> </li> <li> <p><strong>Output_bam</strong><br> Resulting BAM files including unmapped, non-primary aligned, and duplicated (marked) reads.&nbsp;Files are provided in&nbsp;<code>out</code>&nbsp;directory by&nbsp;STRTN.sh.</p> </li> <li> <p><strong>Output_bai</strong><br> Index files (.bai) of the resulting BAM files in the&nbsp;<code>Output_bam</code>&nbsp;directory.&nbsp;Files are provided in&nbsp;<code>out</code>&nbsp;directory by&nbsp;STRTN.sh.</p> </li> <li> <p><strong><code>OUTPUT</code>.output.bam</strong><br> BAM files containing reads except for duplicate and non-primary reads.&nbsp;Files are provided in the working directory by&nbsp;STRTN.sh.</p> </li> <li> <p><strong><code>OUTPUT</code>.minus.bw</strong>&nbsp;and&nbsp;<strong><code>OUTPUT</code>.plus.bw</strong><br> BigWig files for each strands of each sample.&nbsp;Files are provided in the working directory by&nbsp;STRTN.sh.</p> </li> <li> <p><strong>coding_5end.bb</strong><br> BigBed file for coding-5&#39;end annotation file. It is&nbsp;provided in the working directory by&nbsp;STRTN.sh</p> </li> </ul> <ul> <li> <p><strong>hub.txt</strong><br> Parameters for each tracks. It is&nbsp;provided in the working directory by&nbsp;STRTN-UCSC-Allas.sh.</p> </li> <li> <p><strong>Link of hub.txt file</strong><br> Provided by&nbsp;STRTN-UCSC-Allas.sh.</p> </li> <li> <p><strong><code>OUTPUT</code>-QC-BeeswarmPlots.pdf</strong><br> Visualization quality check values for each developmental stage using BeeswarmPlots.&nbsp;It is provided in&nbsp;<code>out</code>&nbsp;directory by STRTN-Seurat.sh.</p> </li> <li> <p><strong>Rplots.pdf</strong><br> Elbow, JackStraw, PCA, UMAP and violin plots.&nbsp;It is provided in&nbsp;<code>out</code>&nbsp;directory&nbsp;by STRTN-Seurat.sh.</p> </li> <li> <p><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.&nbsp;<a href="https://gatk.broadinstitute.org/hc/en-us/articles/360037426491-ExtractIlluminaBarcodes-Picard-">https://gatk.broadinstitute.org/hc/en-us/articles/360037426491-ExtractIlluminaBarcodes-Picard-</a></p> </li> <li> <p><strong>HISAT2_Metrics</strong><br> Alignment summary of samples from each lane produced by the HISAT2 program.&nbsp;<a href="https://daehwankimlab.github.io/hisat2/manual/">https://daehwankimlab.github.io/hisat2/manual/</a></p> </li> <li> <p><strong>MarkDuplicates_Metrics</strong><br> Metrics file indicating the numbers of duplicates produced by the Picard MarkDuplicates program.&nbsp;<a href="https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-">https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-</a></p> </li> <li> <p><strong><code>OUTPUT_</code>MultiQC_report.html&nbsp;</strong><br> For each sample, fastq files&nbsp;from the output BAM files are generated by&nbsp;fastq-fastQC.sh in the&nbsp;<code>fastq</code>&nbsp;directory. These fastq files (without duplicated reads) can be submitted to public sequence databases.&nbsp;<a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a>&nbsp;files are also generated for each fastq file in the&nbsp;<code>fastqc</code>&nbsp;directory. Based on the FastQC results,&nbsp;<a href="https://multiqc.info/">MultiQC</a>&nbsp;report (<strong>MultiQC_report.html</strong>) is generated.</p> </li> <li> <p><strong><code>OUTPUT_</code>byTFE-counts_annotation.txt</strong><br> Read count table output from featureCounts with genomic annotations, produced by STRTN-TFE.sh.</p> </li> <li> <p><strong><code>OUTPUT_</code>peaks.bed</strong><br> Peak position information of TFEs, produced by&nbsp;STRTN-TFE.sh.</p> </li> <li> <p><strong><code>OUTPUT_</code>annotation</strong><br> Annotation of TFEs,&nbsp; produced by&nbsp;STRTN-TFE.sh.</p> </li> </ul>