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Commit 8911a6f7 authored by dilawar's avatar dilawar :ant:
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Added the pipeline.

Run `copr .`
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ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/096/SRR11862696/SRR11862696_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/096/SRR11862696/SRR11862696_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/097/SRR11862697/SRR11862697_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/097/SRR11862697/SRR11862697_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/099/SRR11862699/SRR11862699_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/099/SRR11862699/SRR11862699_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/082/SRR11862682/SRR11862682_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/082/SRR11862682/SRR11862682_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/091/SRR11862691/SRR11862691_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/091/SRR11862691/SRR11862691_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/092/SRR11862692/SRR11862692_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/092/SRR11862692/SRR11862692_2.fastq.gz
\ No newline at end of file
File deleted
a) Sample raw data: enclosed is a text file with dataset download links 1. Sample raw data: enclosed is a text file with dataset download links.
b) file types for inputs and outputs at each step (particularly for FASTQC and TrimGalore (first two steps) operations): enclosed as a table below (also enclosed the corresponding excel file): 2. File types for inputs and outputs at each step (particularly for FASTQC and
S.No. Analysis stage Tool used Input file type Code Output data type TrimGalore (first two steps) operations)
1 Quality check FastQC fq / fastq ./fastqc *fastq.gz text, html QC reports
2 Quality trimming TrimGalore fq / fastq trim_galore --gzip --fastqc --max_n 2 --paired --length 50 SRR11862696_1.fastq.gz SRR11862696_2.fastq.gz fq; fastq Enclosed as a table below (also enclosed the corresponding excel file):
S.No. Analysis stage Tool used Input file type Code Output data type 1 Quality check FastQC fq / fastq ./fastqc
*fastq.gz text, html QC reports 2 Quality trimming TrimGalore fq / fastq
trim_galore --gzip --fastqc --max_n 2 --paired --length 50
SRR11862696_1.fastq.gz SRR11862696_2.fastq.gz fq; fastq
#!/usr/bin/env bash
FILES=$(cat ./data/SampleInputFileLinks.txt)
for file in $FILES; do
# --no-clobber, do not download if file already exists.
wget -nc $file
done
fastqc *fastq.gz
trim_galore --gzip --fastqc --max_n 2 --paired --length 50 \
SRR11862696_1.fastq.gz SRR11862696_2.fastq.gz
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