STAR
https://github.com/alexdobin/STAR------------------------------------------------------------
HTSeq
http://www-huber.embl.de/HTSeq/doc/install.html============================================================
./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:
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
python setup.py build
sudo python setup.py install
(3) Run the command
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S479Aligned.out.sam ../Homo_sapiens.GRCh38.87.gtf > S479.counts