You can place the executables or make symbolic links in a location recognisable by$PATH or make changes to$PATH to avoid needing to specify full paths when using the programs. All codes provided assume executables can be found in $PATH.
* Latest stable version available at the time of writing
$ ./fastqc --help
FastQC - A high throughput sequence QC analysis tool
SYNOPSIS
fastqc seqfile1 seqfile2 .. seqfileN
fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
[-c contaminant file] seqfile1 .. seqfileN
DESCRIPTION
FastQC reads a set of sequence files and produces from each one a quality
control report consisting of a number of different modules, each one of
which will help to identify a different potential type of problem in your
data.
If no files to process are specified on the command line then the program
will start as an interactive graphical application. If files are provided
on the command line then the program will run with no user interaction
required. In this mode it is suitable for inclusion into a standardised
analysis pipeline.
$ wget -O BBMap_38.82.tar.gz 'https://downloads.sourceforge.net/project/bbmap/BBMap_38.82.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fbbmap%2Ffiles%2FBBMap_38.82.tar.gz%2Fdownload&ts=1587572478'
$ tar xvf BBMap_38.82.tar.gz
$ cd bbmap
$ ./bbduk.sh
Written by Brian Bushnell
Last modified March 24, 2020
Description: Compares reads to the kmers in a reference dataset, optionally
allowing an edit distance. Splits the reads into two outputs - those that
match the reference, and those that don't. Can also trim (remove) the matching
parts of the reads rather than binning the reads.
Please read bbmap/docs/guides/BBDukGuide.txt for more information.
Usage: bbduk.sh in=<input file> out=<output file> ref=<contaminant files>
Input may be stdin or a fasta or fastq file, compressed or uncompressed.
If you pipe via stdin/stdout, please include the file type; e.g. for gzipped
fasta input, set in=stdin.fa.gz
$ wget https://github.com/COMBINE-lab/salmon/releases/download/v1.2.1/salmon-1.2.1_linux_x86_64.tar.gz
$ tar xvf salmon-1.2.1_linux_x86_64.tar.gz
$ mv salmon-latest_linux_x86_64 salmon-1.2.1
$ cd salmon-1.2.1/bin
$ ./salmon
salmon v1.2.1
Usage: salmon -h|--help or
salmon -v|--version or
salmon -c|--cite or
salmon [--no-version-check] <COMMAND> [-h | options]
Commands:
index Create a salmon index
quant Quantify a sample
alevin single cell analysis
swim Perform super-secret operation
quantmerge Merge multiple quantifications into a single file
Kallisto is phasing out HDF5 at the time of writing, binaries for this release (v0.46.2) are compiled with HDF5 built in
$ wget https://github.com/pachterlab/kallisto/releases/download/v0.46.2/kallisto_linux-v0.46.2.tar.gz
$ tar zxf kallisto_linux-v0.46.2.tar.gz
$ mv kallisto kallisto-v0.46.2
$ cd kallisto-v0.46.2
$ ./kallisto
kallisto 0.46.2
Usage: kallisto <CMD> [arguments] ..
Where <CMD> can be one of:
index Builds a kallisto index
quant Runs the quantification algorithm
bus Generate BUS files for single-cell data
pseudo Runs the pseudoalignment step
merge Merges several batch runs
h5dump Converts HDF5-formatted results to plaintext
inspect Inspects and gives information about an index
version Prints version information
cite Prints citation information
Running kallisto <CMD> without arguments prints usage information for <CMD>
Download and unpack the file. Use make to compile STAR
$ wget -O STAR-2.7.3a.tar.gz https://github.com/alexdobin/STAR/archive/2.7.3a.tar.gz
$ tar xvf STAR-2.7.3a.tar.gz
$ cd STAR-2.7.3a/source
$ make STAR
$ ./STAR
Usage: STAR [options]... --genomeDir /path/to/genome/index/ --readFilesIn R1.fq R2.fq
Spliced Transcripts Alignment to a Reference (c) Alexander Dobin, 2009-2019
For more details see:
<https://github.com/alexdobin/STAR>
<https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf>
To list all parameters, run STAR --help
$ wget -O RSEM-1.3.3.tar.gz https://github.com/deweylab/RSEM/archive/v1.3.3.tar.gz
$ tar zxf RSEM-1.3.3.tar.gz
$ cd RSEM-1.3.3
By default, RSEM executables are installed to /usr/local/bin. You can change the installation location by setting DESTDIR and/or prefix variables. The RSEM executables will be installed to ${DESTDIR}${prefix}/bin. The default values of DESTDIR and prefix are DESTDIR= and prefix=/usr/local.
$ make
$ make install
$ rsem-calculate-expression
Invalid number of arguments!
NAME
rsem-calculate-expression - Estimate gene and isoform expression from
RNA-Seq data.
SYNOPSIS
rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name
rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name
rsem-calculate-expression [options] --alignments [--paired-end] input reference_name sample_name
Preparing indices
$ cd /home/USER/db/refanno
Salmon index
SAF genome index (recommended)
Full genome is used as decoy, largde index but least prone to spurious alignments
Indexing takes under 40 minutes running on 6 threads, and the index size is 17 GB
Use header-cleaned transcript file to create index
Indexing takes under 6 minutes running on a single thread, and the index size is 3.0G
$ kallisto index -i gencode.v33_kallisto-0.46.2 gencode.v33.transcripts.clean.fa
STAR index
The --sjdbOverhang option is set as 150 in this tutorial. This length should be equal to the ReadLength-1of the fastq files. The STAR manual suggests the ideal value is max(ReadLength)-1 in case of reads of varying length. In most cases, the default value of 100 will work as well as the ideal value.
Indexing takes about 70 minutes running on 6 threads, and the index size is 28 GB