This table lists the files that Tapestri DNA Pipeline generates and a brief description of its contents. For detailed information, refer to this article.
|
File |
Description |
|
allele.drop.out.report.txt |
This text file lists the positions used to calculate the allele dropout (ADO) rate and the minimum requirements needed for the calculation. |
|
barcode.cell.coverage.tsv |
This file lists each amplicon and the number of mean reads per cell. For each amplicon, it also lists whether the amplicon passed the threshold. |
|
barcode.cell.distribution.merged.tsv |
A file that reports the number of forward reads assigned to each amplicon for each cell found for all tubes in a run. For more information, see this file. |
|
barcode.cell.distribution.tsv |
A file that reports the number of forward reads assigned to each amplicon for each cell found. This file is index-specific, meaning for only one tube. |
|
barcode.cumsum.txt |
This text file lists the total cumulative reads for all barcodes to be used for creating the log-log plot in the CellFinder_report.pdf. |
|
CellFinder_report.pdf |
This file contains three plots, which visualize barcode distribution and include details on cell uniformity and amplicon distribution. It is index-specific, meaning for only one tube. For more information, see this file. |
|
cells.loom |
This file is an input file for Tapestri Insights. LOOM is an efficient file format for very large omics datasets, consisting of a main matrix, optional layers, and a variable number of row and column annotations. For more information, see this file. |
|
cells.txt |
Lists all the barcodes called as cells by cellfinder. |
|
cells.vcf.gz |
This compressed annotated .vcf file conforms to the standard GATK format. It contains all the variants for all the barcodes called as cells. |
|
DIR.info |
A text file listing the parameters Tapestri DNA Pipeline used, including minimum values and quality thresholds, GATK version, and directory locations. |
|
DIR.yaml |
A text file listing the parameters for the genome, the directory location, and dependencies for the Tapestri DNA Pipeline run. |
|
flagstat.txt |
This text file shows the mapping statistics from the reference genome alignment step, listing the number of QC-passed reads and QC-failed reads for items like read1, read2, properly paired, and mapped. This file is index-specific, meaning for only one tube. |
|
flt3.itd.report.txt |
This report details the FLT3-ITD variants for each cell. |
|
gatk_progress.csv |
This file shows the GATK progress throughout the run. It displays Done when complete. |
|
index.cells.bam |
This file lists a read group (RG) tag for each read, which can be used to find the number of reads for a barcode. It is index-specific, meaning for only one tube. |
|
index.mapped.bam |
This file is generated after mapping to the reference genome and selecting high-quality primary alignments with a mapping quality score of > 30. It is generated after alignment but before barcode correction or cell calling. It maps all the barcodes and is index-specific, meaning for only one tube. |
|
mapped.target.count.txt |
This file lists the total reads mapped to each barcode. |
|
metadata.csv |
For each tube, this file displays – tube prefix, total reads, reads trimmed, reads mapped to reference genome, reads mapped to insert, cells called, mapping error rate, reads mapped to cells, chemistry version, and flagstat file name. |
|
part2_progress.csv |
This file shows the progress through Part2 of the run and lists all the steps that were successfully executed. |
|
pipeline_input.json |
A text file mapping the tubes and lanes. |
|
pipeline_output.json |
A text file that breaks down metrics by the tube and for the run. For each tube, it displays – total read pairs, % and number of read pairs for valid cells, number of cells found, avg reads per cell, and panel uniformity. For each run, it displays all the information for the tubes consolidated, % dropout rate, and chemistry version. |
|
run.options |
A text file listing the parameters used by DNA Pipeline, such as fastq.gz file names; minimums and maximums for FLT3, ALT alleles, ADO, DP, GQ, AF, and LOD; whitelist; and adapters. |
|
summary.txt |
This file reports the sequencing metrics. For more information, see this file. |
|
tapestri_log.txt |
A detailed report on the individual steps performed by Tapestri DNA Pipeline. |
|
vcf_header.txt |
This file contains all the barcodes that are in the .vcf file and in the same order. |