setQC - A automatic report generating app

Time-stamp: "2017-12-12 13:02:33"

Scripts

1. setQC_wrapper_any.sh:

Input

1. sample.txt: a txt file includes all the sample names for this report.

Output

report link

1. example: http://epigenomics.sdsc.edu:8084/2017-10-25-sswangson_morgridge/07e71bc01fec2c53bdc3776d8ada29cc/chu_hsap/setQC_report_any.html
2. interpretion: http://[base_url][-b][hash][-n]setQC_report_any.html.

Steps

1. run multiQC: runMultiQC.sh:
2. Prepare tracks data:
   • pull tracks from scratch folder to the setQC/data folder
   • get individual tracks.json files and cat togaher
   • make track json: genWashUtracks.R:
     • input set_dir: dir under the base
3. Calculate fc over the merged peak locations calcOverlapAvgFC.sh
   • make merged peak bed
   • clip and sort the bed
   • bigWigAvergaeOverBed to generate avgOverlapFC.tab file
4. generate setQC report
   • need to be bds_atac_py3 environment
5. uploading files to server
   • regular files: create by cp -rs
   • apps

setQC reports:

1. Sample info
2. Fastq QCs
3. Mappability
4. Peaks
5. LibQC tables
6. tracks
7. data files

run script

setQC_wrapper_any.sh -s ~/scratch/others/2017-10-25-sswangson_morgridge/chu_hsap/uniq_samples_rev.txt \
    -b 2017-10-25-sswangson_morgridge -n chu_hsap -l ~/scratch/others/2017-10-25-sswangson_morgridge/chu_hsap/