Create a conda environmanet with python 2.7. I installed DEXSeq in via conda in python3 but used the script in python2,7 environment because fo the syntax error.
Preparing the DEXSeq compatible gff. We wish to generate nonoverlapping aggregate gtf. For details refer here.
In the process of forming the counting bins, the script might come across overlapping genes. If two genes on the same strand are found with an exon of the first gene overlapping with an exon of the second gene, the script’s default behaviour is to combine the genes into a single “aggregate gene” which is subsequently referred to with the IDs of the individual genes, joined by a plus (‘+’) sign. If you do not like this behaviour, you can disable aggregation with the option
-r no. Without aggregation, exons that overlap with other exons from different genes are simply skipped.
python /home/parashar/anaconda3/lib/R/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py -r no /home/parashar/archive/rnaseq/gencode.v33.annotation.gtf gencode.v33.gff 2> gff.stderr
DEXSeq doesnot work with BAM files though they claim it can. So convert the bams to sam files using samtools view subcommand.
while read p
do
name=$(basename ${p} .sorted.sam)
bsub -o $name.o -e $name.e -n 10 -q regularq "python /home/parashar/anaconda3/lib/R/library/DEXSeq/python_scripts/dexseq_count.py -p yes -r pos -s reverse -a 10 gencode.v33.gff $p ${name}.Readcounts.txt 2> ${name}.stderr"
done < list
Difference between the expression and exon usgae can be understood from here and here