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[ngstool]

STAR
https://github.com/alexdobin/STAR
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HTSeq
http://www-huber.embl.de/HTSeq/doc/install.html
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./STAR --genomeDir ../GRCh38/  --runThreadN 4 --readFilesIn SRR980479_1.fastq SRR980479_2.fastq --outFileNamePrefix S479
Mar 15 12:31:30 ..... started STAR run
Mar 15 12:31:30 ..... loading genome
Mar 15 12:45:10 ..... started mapping
Mar 15 12:45:42 ..... finished successfully

HTSeq
(1) Make sure that the standard GNU build environment installed. Users of Ubuntu Linux simply type:

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sudo apt-get install build-essential python2.7-dev python-numpy python-matplotlib
(2) Install HTSeq. Download the source package from https://pypi.python.org/pypi/HTSeq, unpack the tarball, go into the directory with the unpacked files and type there

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python setup.py build
sudo python setup.py install
(3) Run the command

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htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S479Aligned.out.sam ../Homo_sapiens.GRCh38.87.gtf > S479.counts