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[admin]

https://benchtobioinformatics.wordpress.com/category/htseq-count/
http://www-huber.embl.de/users/anders/HTSeq/doc/install.html
samtools view -b -S D042Aligned.out.sam > D042Aligned.bam
samtools sort D042Aligned.bam D042Aligned-sorted
samtools index D042Aligned-sorted.bam

samtools view -b -S D040Aligned.out.sam > D040Aligned.bam
samtools sort D040Aligned.bam D040Aligned-sorted
samtools index D040Aligned-sorted.bam

samtools view -b -S D041Aligned.out.sam > D041Aligned.bam
samtools sort D041Aligned.bam D041Aligned-sorted
samtools index D041Aligned-sorted.bam

samtools view -b -S D017Aligned.out.sam > D017Aligned.bam
samtools sort D017Aligned.bam D017Aligned-sorted
samtools index D017Aligned-sorted.bam

samtools view -b -S D002Aligned.out.sam > D002Aligned.bam
samtools sort D002Aligned.bam D002Aligned-sorted
samtools index D002Aligned-sorted.bam

samtools view -b -S D007Aligned.out.sam > D007Aligned.bam
samtools sort D007Aligned.bam D007Aligned-sorted
samtools index D007Aligned-sorted.bam

samtools view -bf 1 D002Aligned-sorted.bam > D002.bam
samtools view -bf 1 D007Aligned-sorted.bam > D007.bam
samtools view -bf 1 D017Aligned-sorted.bam > D017.bam
samtools view -bf 1 D040Aligned-sorted.bam > D040.bam
samtools view -bf 1 D041Aligned-sorted.bam > D041.bam
samtools view -bf 1 D042Aligned-sorted.bam > D042.bam

htseq-count -m union -r pos -i gene_name -a 10 --stranded=no D002.bam ~/Homo_sapiens.GRCh38.84.gtf > D002.counts

[ngstool]

sudo apt-get install python python-setuptools python-pip python-matplotlib cython zlib1g-dev 
sudo pip install biopython
sudo pip install pysam

https://pypi.python.org/pypi/HTSeq

[ngstool]

htseq-count -m union -r pos -i gene_name -a 10 --stranded=no E826Aligned.out.sam ~/Homo_sapiens.GRCh38.84.gtf > E826.counts