STRT-N mouse library output files
Output files from STRT-N data analysis
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:
OUTPUT-QC.txt
Quality check report for all samples. It is provided in out directory by STRTN.sh.
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. It is provided in out directory by STRTN.sh.
Please consider these outlier samples for the further downstream analysis.
OUTPUT_byGene-counts.txt
Read count table output from. It is provided in out directory by STRTN.sh.
featureCounts. https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf
OUTPUT_byGene-counts.txt.summary
Filtering summary from. It is provided in out directory by STRTN.sh.
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. Files are provided in out directory by STRTN.sh.
Output_bai
Index files (.bai) of the resulting BAM files in the Output_bam directory. Files are provided in out directory by STRTN.sh.
OUTPUT.output.bam
BAM files containing reads except for duplicate and non-primary reads. Files are provided in the working directory by STRTN.sh.
OUTPUT.minus.bw and OUTPUT.plus.bw
BigWig files for each strands of each sample. Files are provided in the working directory by STRTN.sh.
coding_5end.bb
BigBed file for coding-5'end annotation file. It is provided in the working directory by STRTN.sh
hub.txt
Parameters for each tracks. It is provided in the working directory by STRTN-UCSC-Allas.sh.
Link of hub.txt file
Provided by STRTN-UCSC-Allas.sh.
OUTPUT-QC-BeeswarmPlots.pdf
Visualization quality check values for each developmental stage using BeeswarmPlots. It is provided in out directory by STRTN-Seurat.sh.
Rplots.pdf
Elbow, JackStraw, PCA, UMAP and violin plots. It is provided in out directory by STRTN-Seurat.sh.
ExtractIlluminaBarcodes_Metrics
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-
HISAT2_Metrics
Alignment summary of samples from each lane produced by the HISAT2 program. https://daehwankimlab.github.io/hisat2/manual/
MarkDuplicates_Metrics
Metrics file indicating the numbers of duplicates produced by the Picard MarkDuplicates program. https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-
OUTPUT_MultiQC_report.html
For each sample, fastq files from the output BAM files are generated by fastq-fastQC.sh in the fastq 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 fastqc directory. Based on the FastQC results, MultiQC report (MultiQC_report.html) is generated.
OUTPUT_byTFE-counts_annotation.txt
Read count table output from featureCounts with genomic annotations, produced by STRTN-TFE.sh.
OUTPUT_peaks.bed
Peak position information of TFEs, produced by STRTN-TFE.sh.
OUTPUT_annotation
Annotation of TFEs, produced by STRTN-TFE.sh.