abnerchang/subset repository overview

Demo:

C:\Users\abner>docker images REPOSITORY TAG IMAGE ID CREATED SIZE ubuntu 16.04 747cb2d60bbe 2 weeks ago 122MB ubuntu 14.04 dea1945146b9 5 weeks ago 188MB d4w/nsenter latest 9e4f13a0901e 13 months ago 83.8kB

C:\Users\abner>docker run abnerchang/subset /ngs/peQdist Unable to find image 'abnerchang/subset:latest' locally latest: Pulling from abnerchang/subset ae79f2514705: Already exists 5ad56d5fc149: Already exists 170e558760e8: Already exists 395460e233f5: Already exists 6f01dc62e444: Already exists 742d9b15c821: Already exists 277f7458c8a8: Pull complete Digest: sha256:222fdd84d0bf26253b04263f136f9a8b98b3fdfab5f77cfe4be8dbf3b202e0b3 Status: Downloaded newer image for abnerchang/subset:latest === peQdist: Read PE-FASTQ files and generate quality distribution and GC% of paired-end FASTQ files ===

Usage: peQdist r1.fq r2.fq outPrjName Verson: 0.9 (2017/10) Author: Yu-Jung Chang

C:\Users\abner>docker run -v C:\Users\abner\data:/data abnerchang/subset /ngs/peQdist /ngs/testdata/test-r1.fq /ngs/testdata/test-r2.fq /data/test-dist --- Summary of PE FASTQ --- InputFile: /ngs/testdata/test-r1.fq,/ngs/testdata/test-r2.fq #PE: 250 #Read: 500 #Base: 114165 AvgReadLen: 228.33 MinReadLen: 35 MaxReadLen: 251 OutFile: /data/test-dist.csv,/data/test-dist.htm

C:\Users\abner>docker run -v C:\Users\abner\data:/data abnerchang/subset /ngs/peQsubset /ngs/testdata/test-r1.fq /ngs/testdata/test-r2.fq /data/test-subset_MinQ7 100 7 --- Summary --- PE's '%HighQ(7) >= 100.0 Name,Original,Subset,Sub/Ori #PE,250,119,47.6% #Base,114165,51844,45.4% AvgReadLen,228.3,217.8,95.4% MaxReadLen,251,251,100.0% MinReadLen,35,35,100.0% BaseQmean,31.4,34.4,109.5% OutFile: /data/test-subset_MinQ7.csv,/data/test-subset_MinQ7-r1.fq,/data/test-subset_MinQ7-r2.fq