Idowu Olawoye idolawoye
kapsakcj
/ concatenate-barcoded-nanopore-reads.sh
Last active
December 10, 2025 09:29
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #!/bin/bash | |
| # by: Curtis Kapsak ([email protected]) | |
| # 2021-07-30; updated 2022-03-03 | |
| # | |
| # This script is for concatenating fastq.gz files that from a Nanopore sequencing run, | |
| # specifically with barcoded/multiplexed sequencing runs. It will not overwrite the original fastq files, but rather | |
| # concatenate fastqs for each barcoded sample, and write them to a single output directory. | |
| # | |
| # REQUIREMENTS: | |
| # This script requires that fastq.gz files are arranged in the normal output/directory |
EpiDemos82
/ Useful_BASH_commands.txt
Last active
March 1, 2023 19:01
Useful BASH commands for working with NGS data
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ##GENERAL TEXT OR FILE MANIPULATION | |
| #Find lines in a list (e.g. file names) that are not present in another list | |
| #This is good for checking whether downstream files are present (i.e. pipeline ran susscessfully) | |
| comm -23 <(sort All.txt) <(sort Finished.txt) | |
| #Looping over anything | |
| for f in $(cat names.txt); do whatever to ${f}; done | |
| #renaming file extensions using bash code |