Since the whole dataset is too big to upload into Github, this repository includes intermediate results and source code for this work.
The result, source code and data for each organism/cell line are stored seperatelly in each folder.
K562 stores source code, motifs and cryptic splice sites related to K562 cell line in humans.
HepG2 stores source code, motifs and cryptic splice sites related to HepG2 cell line in humans.
mouse stores source code, motifs and cryptic splice sites related to N2A and CGR8 cell lines in mice.
fly stores source code, motifs and cryptic splice sites related to S2 cell line in fruit flies.
code stores source codes.
STAR aligner will output SJ files, which is very convient for splice junction analysis.
Read count support cryptic splice sites account 5/10,000 of total mapped reads in average, this make sensitivity is key thing to consider when analyzing cryptic splice sites. Thus I choose STAR with 2-pass mode to do alignment since it can detect highest number of cryptic splice sites. the sub-folders that starts with star are related to cryptic splice sites.
star_target_only_jc stores the position of cryptic junctions.
star_target_only_jc_5ss stores the position of cryptic 5' splice sites.
star_target_only_jc_3ss stores the position of cryptic 3' splice sites.
The jI tag in the STAR aligner, contain the junction sites, the regions between the junction sites are either introns or exons. I used this method to extract exon regions.
exon_mer_target_only stores the postion of cryptic exons.
exon_mer_target_only_5ss stores the position of cryptic exons' 5' splice sites.
I store cryptic splice sites' motifs of different regions in different folders.
star_abs3_motif stores the motifs of cryptic splice 3' splice sites for each shRNA-seq.
star_abs5_motif stores the motifs of cryptic splice 5' splice sites for each shRNA-seq.
star_abs3_motif_canonical stores the motifs of cryptic splice 3' splice sites near canonical splice sites for each shRNA-seq.
star_abs5_motif_canonical stores the motifs of cryptic splice 5' splice sites near canonical splice sites for each shRNA-seq.
star_abs3_motif_exon stores the motifs of cryptic splice 3' splice sites in exon regions for each shRNA-seq.
star_abs5_motif_exon stores the motifs of cryptic splice 5' splice sites in exon regions for each shRNA-seq.
star_abs3_motif_deep_intron stores the motifs of cryptic splice 3' splice sites in deep introns for each shRNA-seq.
star_abs5_motif_deep_intron stores the motifs of cryptic splice 5' splice sites in deep introns for each shRNA-seq.
The pdf file in each cell line's directory
The meta-profiles of cryptic sites in K562, “3_” indicates cryptic 3' splice sites, while “5_” indicates cryptic 5' splice sites. Three panels in each figure: the first panel is the metaprofile of 5' splice sites, where 0 is the 5' splice site position; the second panel is the metaprofile of 3' splice sites, where 0 is the 3' splice site position; the third panel is around the brand point, where 0 is the branch point position.