Skip to content

added a section for samtools and some grep commands #28

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
karimhussein1 wants to merge 2 commits into
base: master
Choose a base branch
from
Open

added a section for samtools and some grep commands #28

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
1fb4f85
added a section for samtools and some grep commands
karimhussein1 Sep 9, 2023
7a941db
minor
karimhussein1 Sep 9, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
79 changes: 74 additions & 5 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

[![DOI](https://zenodo.org/badge/3882/stephenturner/oneliners.svg)](https://zenodo.org/badge/latestdoi/3882/stephenturner/oneliners)

Useful bash one-liners useful for bioinformatics (and [some, more generally useful](#etc)).
Useful bash one-liners useful for bioinformatics (and [some, more generally useful](#etc)).


## Contents
Expand All @@ -13,6 +13,7 @@ Useful bash one-liners useful for bioinformatics (and [some, more generally usef
- [sort, uniq, cut, etc.](#sort-uniq-cut-etc)
- [find, xargs, and GNU parallel](#find-xargs-and-gnu-parallel)
- [seqtk](#seqtk)
- [Samtools](#Samtools)
- [GFF3 Annotations](#gff3-annotations)
- [Other generally useful aliases for your .bashrc](#other-generally-useful-aliases-for-your-bashrc)
- [Etc.](#etc)
Expand Down Expand Up @@ -209,7 +210,7 @@ Decouple an interleaved fastq file:
| tee >(cut -f 1-4 | tr '\t' '\n' > reads-1.fastq) \
| cut -f 5-8 | tr '\t' '\n' > reads-2.fastq

## sort, uniq, cut, etc.
## sort, uniq, cut, grep, etc.

[[back to top](#contents)]

Expand Down Expand Up @@ -265,7 +266,27 @@ Take a fasta file with a bunch of short scaffolds, e.g., labeled `>Scaffold12345

Display hidden control characters:

python -c "f = open('file.txt', 'r'); f.seek(0); file = f.readlines(); print file"
python -c "f = open('file.txt', 'r'); f.seek(0); file = f.readlines(); print file"


Count the number of sequences in a FASTA file

grep -c "^>" sequence.fasta


Extract sequences with a specific ID from a FASTA file:

grep -A1 -w "desired_ID" your_sequence.fasta


Find lines in a GFF file associated with a particular feature like a "gene for example":

grep -w "gene" annotation_file.gff


Filter VCF (Variant Call Format) lines based on a specific chromosome

grep "^chr1" variants_file.vcf


## find, xargs, and GNU parallel
Expand Down Expand Up @@ -391,6 +412,55 @@ Untangle an interleaved paired-end FASTQ file. If a FASTQ file has paired-end re
seqtk seq -l0 -2 interleaved.fq > deinterleaved_2.fq


## Samtools

[[back to top](#contents)]

Download samtools at [samtools](https://github.com/samtools/samtools). Samtools is a set of utilities for interacting with and manipulating files in the SAM (Sequence Alignment/Map) format for next-generation sequencing data


Count the number of reads in a SAM/BAM file:

samtools view -c file.bam


Calculate the average mapping quality in a BAM file:

samtools view -F 4 file.bam | awk '{sum += $5} END {print sum / NR}


Sort a BAM file by coordinates:

samtools sort file.bam -o sorted_file.bam


Index a BAM file:

samtools index file.bam


Convert a BAM file to SAM:

samtools view -h -o output.sam input

Or

samtools view -h input.bam > output.sam


Convert a SAM file to BAM:

samtools view -bS file.sam -o output_file.bam


Merge multiple BAM files into one:

samtools merge merged_output.bam file1.bam file2.bam file3.bam


Remove duplicates from a sorted BAM file:

samtools rmdup sorted_file.bam deduplicated_file.bam


## GFF3 Annotations
Expand Down Expand Up @@ -457,7 +527,7 @@ Browse 'up' and 'down'
Ask before removing or overwriting files:

alias mv="mv -i"
alias cp="cp -i"
alias cp="cp -i"
alias rm="rm -i"


Expand Down Expand Up @@ -625,4 +695,3 @@ Exclude a column with cut (e.g., all but the 5th field in a tab-delimited file):
Find files containing text (`-l` outputs only the file names, `-i` ignores the case `-r` descends into subdirectories)

grep -lir "some text" *