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@@ -142,7 +142,7 @@ After defining unique features (TSSs, exons and PASs) and identifying the number
 >      - coverage
 >      - alignment-based counts
 > - Gencode gene
-> - flag for Gencode match (i.e., =, c, j
+> - flag for Gencode match (i.e., =, c, j)
 > - bonferroni adjusted p-values. <br>
 
 <p align="right"> [`TOP`](#full-length-mrna-sequencing-uncovers-a-widespread-coupling-between-transcription-and-mrna-processing)</p><br>
@@ -169,7 +169,17 @@ This analysis was performed to identify loci that contain tandem 3' UTRs (loci w
 ## **Sequence Motif Analysis Relative to Acceptor and Donor Sites** <br>
 For each detected gene, we report the first and last nucleotide of each exon as acceptor and donor splice sites, respectively. Each unique genomic position was converted into a BED format and the strand specific sequences of 2 nucleotides were extracted using UCSC Table Browser (GRCh37/hg19) for both acceptor and donor splice sites. 
 
-> **`script:`** The python script for extracting dinucleotide sequences of the splice-sites at R1 and R3 domains (i.e., canonical GT and AG motifs) can be found [**here**](https://git.lumc.nl/s.y.anvar/mRNA-Coupling/ipython_notebook/master/scripts/Rdomain_splice_junction_motif.ipynb). <br>
+> **`script:`** The python script for extracting dinucleotide sequences of the splice-sites at R1 and R3 domains (i.e., canonical GT and AG motifs) can be found [**here**](https://git.lumc.nl/s.y.anvar/mRNA-Coupling/ipython_notebook/master/scripts/Rdomain_splice_junction_motif.ipynb). <br> <br>
+> **input** <br> [:arrow_down:]() FASTA files, intronic sequences of R1 and R3 domains. Sequence headers contains additional information regarding the coupling of the exon with other features, etc. <br> <br>
+> **output** <br> [:arrow_up:]() Text file containing information on:
+> - gene id
+> - genomic position
+> - exon id/name
+> - coupling info
+> - exons sharing the R1 domain
+> - exons sharing the R3 domain
+> - R1 splicing motif (acceptor)
+> - R3 splicing motif (donor) <br>
 
 <p align="right"> [`TOP`](#full-length-mrna-sequencing-uncovers-a-widespread-coupling-between-transcription-and-mrna-processing)</p><br>