This directory contains output and required files in use-cases.

For manual on specific web tools in refTSS, please visit: 
https://reftss.riken.jp/reftss/Manual

For question and inquiries about the data please contact:
reftss-help@riken.jp 

Last update: 2024.10.02


[Directories]
  - analysis_result_files: output files from TSS differential expresson analysis 
  - required_files: required files for each tools in the use case.

[Files in analysis_result_files]
# The all files generated from the data processing within use-case workflow.
  - fastqc_res.tar: result of fastqc process
  - TSS.qcbarplot.pdf: barplot for TSS enrichment quality assessment using GENCODE promoter coordinates
  - tssl.count.matrix.txt.gz: TSS count data matrix of example data
  - maplot.pdf: MA-plot of example data set (Mutant A vs. WT)
  - up/down_det.list.txt: ID list of differentially expressed TSS.
  - reftss_count folder: this folder contains ctss (ctss.txt) and bigWig (bw) files generated from TSS tag-counting against refTSS4 coorinates.

[Files in required files]
  - gencode.v40.promoter300-100.bed.gz: GENCODE promoter coordinates genearated from GRCh38 version 40 gene annotation. Promoter region was extracted from 5'-end of transcript (from -300 to +100).
  - GRCh38.p14.genome: genome size list of GRCh38p14 genearated by faidx program.