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Linux Commands for Bioinformatics Tutorial

This tutorial provides instructions for converting a FASTQ file to FASTA format. It begins with downloading sequencing data in FASTQ format from the European Nucleotide Archive. It then demonstrates how to view and manipulate the FASTQ file using various Linux commands like gzip, cat, grep, awk, sort. The reads are extracted from the FASTQ file and converted to a tabular format for further processing. Unique sequences are identified and sorted before being converted to a FASTA file with the sequence headers and sequences in the appropriate format.

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usef gadallah
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49 views3 pages

Linux Commands for Bioinformatics Tutorial

This tutorial provides instructions for converting a FASTQ file to FASTA format. It begins with downloading sequencing data in FASTQ format from the European Nucleotide Archive. It then demonstrates how to view and manipulate the FASTQ file using various Linux commands like gzip, cat, grep, awk, sort. The reads are extracted from the FASTQ file and converted to a tabular format for further processing. Unique sequences are identified and sorted before being converted to a FASTA file with the sequence headers and sequences in the appropriate format.

Uploaded by

usef gadallah
Copyright
© All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd

Introduction to Bioinformatics “CSCI-471”

Revision for what taken last lab:

1- Determine your path: By using print working directory (pwd)

2- Change your path: By using change directory (cd)

3- Move to Documents and make 2 new folders (lab/lecture): By using mkdir lab lecture

4- Move to lab folder and make txt file called lab tutorial to type some sequences: By using

-cd lab

-cat > [Link] (to make a file and type inside it)

AAAAAACCTGG

GGTCACTGGTA

- cat [Link] (to show its contents)

- cat >> [Link] (to append some data inside this file)

ACGTGGGCCGT

-cat [Link] (to show all its components)

AAAAAACCTGG

GGTCACTGGTA

ACGTGGGCCGT

5- Move to lecture folder (by relative path): cd ../lecture/

6- Make 2 txt files inside lecture folder: touch [Link] [Link]

7- To determine the components of lecture folder: use ls + its arguments (known by use man
ls)

8- Return back to lab folder (by absolute path): cd ~/Documents/lab

9- To determine any details about any commands: man ls or ls --help or google it


This tutorial: case study “change Fastq to Fasta”

#Download Data: By using

wget [Link]

If wget is not found on PC use

yum install wget (or) sudo apt-get install wget

# To determine the components with their space: ls –lh (30M)

# File compression and decompression:

gunzip ERR000001_1.[Link]

# To determine the components with their space: ls -lh (130M)

# Display the Contents of a File

cat ERR000001_1.fastq

more ERR000001_1.fastq

less ERR000001_1.fastq

head ERR000001_1.fastq

tail ERR000001_1.fastq

#Count the Number of Lines

wc ‐l ERR000001_1.fastq

#Search a Pattern (don't determine the read)

grep "CCCCCTTAAAAA" ERR000001_1.fastq

#combine multiple commands

grep “CCCCCTTAAAAA” ERR000001_1.fastq | wc -l

#Converting a FASTQ File into a Tabular Format

cat ERR000001_1.fastq | paste - - - - > ERR_tab.txt

# to determine the difference between both file fastq file and its tabular: head both

# search pattern again (determine the read)

grep "CCCCCTTAAAAA" ERR_tab.txt

#Pattern Matching Using Awk

Its format: awk ‘/pattern to search/ {Actions}’ filename [ awk here make like grep ]

awk '/CCCCCTTAAAAA/ {print $0}' ERR_tab.txt ( $0: print all record) (determine the read)
# To print the first and third record (header and sequence)

awk '/CCCCCTTAAAAA/ {print $1 "\t" $3}' ERR_tab.txt

# To print the sequence and quality score?????? (try by yourself “assignment”)

# To determine which sequences has N

awk '{if($3~"N") print $1 "\t" $3}' ERR_tab.txt #to determine how many sequences????

(try by yourself “assignment”)

#Sort and Extract Unique Sequences

cat ERR_tab.txt | sort -k 3 > ERR_sorted.txt (k to sort specific column here the third column
which is sequences)

#to get the unique sequences

cat ERR_tab.txt | sort -k 3 –u > ERR_unique.txt

# to determine the difference between the sorted and unique files: use wc -l

# Convert Reads into FASTA Format Sequences

awk '{print $1 "\t" $3}' ERR_tab.txt > ERR_allseqs.txt

sed 's/@/>/' ERR_allseqs.txt

head ERR_allseqs.txt

awk '{print $1, "\n" $2}' ERR_allseqs.txt > ERR_allseqs.fasta

head ERR_allseqs.fasta

References:

- [Link]

- [Link]

- [Link]

- [Link]

- [Link]

- [Link]

- Second chapter in Bioinformatics a practical handbook of next generation sequencing


and its [Link]

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