Daily NGS tools for bioinformaticians
User friendly GEO upload. See details below:
> ./uploadGEO.sh -h
This script uploads your folder to GEO FTP server. If the connection times out, it tries to reconnect.
Be careful with your input parameters (especially with -r) to avoid overwhelming the GEO FTP server.
Usage: uploadGEO.sh [FLAGS]
[-l <local_directory>] Local directory to be uploaded [default=.]
[-r <remote_directory>] Remote directory on GEO FTP server
[-u <username>] GEO username
[-p <password>] GEO password
[-h <help>] Print help and exit
For GEO username and password, please refer to https://www.ncbi.nlm.nih.gov/geo/info/submissionftp.html
Example usage:
./uploadGEO.sh -l /my/folder/to/upload/geo -r ./my/geo/directory -u geoftp -p PaSsWoRd
Runs md5sum parallel. -n can be set to 4 times of the cores available (e.g. -n 32 if you have 8 cores on your machine).
./md5parallel.sh -h
Usage: md5parallel.sh [FLAGS]
[-w <working_directory>] Working directory where the MD5SUMS will be checked [default=.]
[-n <n_jobs>] Number of parallel jobs [default=1]
[-o <output_file>] Output filename [default=./md5.txt]
[-g <gzip_file>] Flag to gzip the output file
[-r <remove_working_directory_prefix] Flag for removing the working directory prefix in MD5SUM output file
Merges lane-split FASTQ files. See below:
Usage: fastq_merge.sh [FLAGS]
[-i <input_dir>]
Input directory where FASTQ files to be merged are located
default: .
[-a <sequencing_type>]
Sequencing type: Paired-end (PE) or Single-end (SE)
default: PE
options: PE,SE
[-b <file_basename_pattern>]
Grep pattern for FASTQ files
default: fastq.gz
[-f <file_R1_pattern>]
Grep pattern for FASTQ files with R1_reads
default: R1.fastq.gz
[-r <file_R2_pattern>]
Grep pattern for FASTQ files with R2_reads. Does not influence anything if sequencing type (-a) is SE
default: R2.fastq.gz
[-s <file_basename_seperator>]
Delimitter to seperate FASTQ file basename
default: _ (underscore)
[-c <file_cut_uniq>]
Cut basename of FASTQ file using -s flag. Will be passed to 'cut -f'
default: 1-3
[-t <threads>]
Number of threads to be used for parallel processing
default: 1
[-o <output_dir>]
Input directory for the merged FASTQ files
default: .
[-h help]
Display help menu
Example:
- Files to merge:
001_100_S1_L001_R1.fq.gz
001_100_S1_L002_R1.fq.gz
001_100_S1_L003_R1.fq.gz
001_100_S1_L004_R1.fq.gz
- Output file:
001_100_S1.fq.gz
- Code to run:
fastq_merge.sh -b fq.gz -s _ -c 1-3 -f R1.fq.gz
Extract read length of a gzipped FASTQ file
Usage:
./fastq_readlength.sh myfile.fastq.gz
Converts DNA methylation coverage files (.cov) generated by Bismark to BEDGRAPH files.
Usage: cov2bedgraph.sh [FLAGS]
Examples:
cov2bedGraph -i myfile.cov -o myfile.bedgraph
cov2bedGraph -i myfile.cov -g -o myfile.bedgraph.gz
Flags:
[-i <input_file>] Input cov file. Can be gzipped (.cov.gz). [1-based coord]
[-o <output_file>] Output bedGrapgh file
[-z <zero_based>] Flag if input cov file is in 0-based genomic coordinate. Normally cov files are 1-based, but it can be 0-based in special occasions.
[-g <gzip_file>] Flag to gzip the output file
Extracts the index sequence counts from a gzipped FASTQ file
Usage:
./illumina_indexExtractor.sh myfile.fastq.gz
Find the 'fastq.gz.temp' files.
Usage:
./find_basespace_temp.sh
Removes spaces in the files
Usage:
./removeFilenameSpace.py 'my file.txt'
# Output: myfile.txt
Create ENSEMBL IDs from GTF file. Output columns: gene, transcript, exon, gene name
Usage:
gtf2ensembl.sh [FLAGS]
Description:
Create ENSEMBL IDs from GTF file. Output columns: gene, transcript, exon, gene name
Examples:
gtf2ensembl.sh -i myfile.gtf -o myfile.txt
Flags:
[-i <input_file>] Input gtf file. Can be gzipped (.gtf.gz)
[-o <output_file>] Output file, tab-delimitted
[-g <gzip_file>] Flag to gzip the output file
[-h <help>] Print help
Dependencies:
bedops --> convert2bed