long-read RNA-seq quantification using espresso¶

Summary¶

long-read RNA-seq quantification using espresso 1.6.0, this is a required step to run rMATs-long.

Aligned bam files. Save as samples.tsv in your working dir. ALso need .bai in current dir. Abs path.

/path/to/first.sorted.bam       first_sample_name
/path/to/second.sorted.bam      second_sample_name

hpcf_interactive.sh

module load python/2.7.13

# cd to your working dir

run_lsf.py -p pacbio_expresso

In the jobID folder, see esp file

cd $jid/work_dir

Prepare compare.tsv, a 3-col tsv file, showing samples for group 1 (col1) and samples for group 2 (col), and a comparison name.

The sample names must be the exact sample name you used for expresso analysis.

CD34_P0_rep1,CD34_P0_rep2       CD34_P1_rep1,CD34_P1_rep2       P1_vs_P0
CD34_P0_rep1,CD34_P0_rep2       CD34_P2_rep1,CD34_P2_rep2       P2_vs_P0

hpcf_interactive.sh

module load python/2.7.13

# cd to your working dir

run_lsf.py -f compare.tsv -p rmat_long