retina_specific_exons

Retina specific exons

We compared our results to previous reserach by looking for previously identfiied retina-specific exons in the PacBio retina transcriptome.

Data

• exons.gtf - GTF file with all exons from the PacBio data
• long_exons.bed and short_exons.bed contain retina specific exons idenified by Ciampi et al.
• Musashi.bed contains photoreceptor specific exons in mice identified by Muprhy et al.

Commands

The exons from the PacBio data were extracted with awk

awk -F "\t" '$3=="exon"' \
../data/transcriptomics/isoquant_aln.sorted.transcript_models.gtf \
> exons.gtf

We used bedtools intersect to determine which retina-specific exons were present in the PacBio data

bedtools intersect -u -f 1 \
-a short_exons.bed \
-b exons.gtf \
> overlap_short_exons.bed

bedtools intersect -u -f 1 \
-a long_exons.bed \
-b exons.gtf \
> overlap_long_exons.bed

bedtools intersect -u -f 1 \
-a Musashi.bed \
-b exons.gtf \
> overlap_musashi.bed