compute delta psi

Spent a whole month to get delta psi from AS events but didn't work. Use another approach!

After getting the tpm from bud count.gtf files and flower count.gtf files, merge them by suppa joinFiles. TPM files will be used for psi calculation.

Calculate isoform psi

suppa.py psiPerIsoform -g ../5_stringtie/StringTie/p_persica_stringtie_merged.gtf -e bud.tpm.tpm -o bud_isoform

suppa.py psiPerIsoform -g ../5_stringtie/StringTie/p_persica_stringtie_merged.gtf -e flower.tpm.tpm -o flower_isoform

Output bud_isoform_isoform.psi and flower_isoform_isoform.psi. This time they are not 1 or nan anymore!

Generate ioi file for AS events

suppa.py generateEvents -i ../5_stringtie/StringTie/p_persica_stringtie_merged.gtf -o P_persica_events -f ioi

Output file P_persica_events.ioi for diffSplice.

Calculate delta psi

Using the bud tpm and psi, flower tpm and psi, along with the ioi file, compute delta psi.

suppa.py diffSplice --method empirical --input P_persica_events.ioi --psi bud_isoform_isoform.psi flower_isoform_isoform.psi --tpm bud.tpm.tpm flower.tpm.tpm --area 1000 --lower-bound 0.05 -pa -gc -c -o peach1

Output file peach1.dpsi contain the delta psi value and adjusted p-value. This will be used later to extract isoforms with significant delta PSI. Compare those isoforms with the AS event ioe to know what isoform is under which event.