Final README adjustments

README.md

@@ -8,7 +8,7 @@ conda env create -f requirements.yml
 ```
 ## Required input data
 * VCF file of variants for further annotation
-* BED file with available uORFs (`sorted.v3.bed` in this repository)
+* BED file with available uORFs (`sorted.v4.bed` in this repository)
 * GTF file with genomic features annotation
 * \[optional\] TSV file with gene-level gnomAD constraint statistics
 
@@ -26,7 +26,8 @@ python uORF_annotator.py \
 ```
 ## Output formats specification
 ### tab-separated (tsv) file
-Each row represents annotation of a single variant in particular uORF (per uORF annotation). Fields in the file have the following content:
+
+Two TSV outputs are generated - one for ATG-started uORFs and one - for non-ATG-started ones. Each row represents annotation of a single variant in particular uORF (per uORF annotation). Fields in the file have the following content:
 
 1) #CHROM - contig name  
 2) POS - position  
@@ -52,16 +53,21 @@ Each row represents annotation of a single variant in particular uORF (per uORF
 The generated VCF output contains all variants affecting uORF sequences. Each variant is annotated with the following INFO fields: `uORFs`, `uORFs_ATG`, `uORFs_eff`. The description of fields is given below:
 
 * `uORFs` - a full consequence annotation for each variant-uORF combination. Format: 'ORF_START|ORF_END|ORF_SYMB|ORF_CONSEQ|main_cds_effect|in_known_CDS|in_known_ORF|utid|overlapping_type|dominance_type|codon_type'
-* `uORFs_ATG` - a flag indicating if a variant falls within ATG-starting uORF.
-* `uORFs_eff` - a short notation of main CDS effect. ext - N-terminal extension, overl - out-of-frame overlap, activ - overlap removal with possible main ORF activation, unaff - no effect on main CDS.
+* `uORFs_ATG` - a flag indicating if a variant falls within at least one ATG-starting uORF.
+* `uORFs_eff` - a short notation of how a change in uORF structure resulting from a variant affects the main coding part (СDS) of a gene. ext - N-terminal extension, overl - out-of-frame overlap, activ - overlap removal with possible main ORF activation, unaff - no effect on main CDS. If the variant falls into more than one uORF, the effects on them are listed through &
 
 ### BED format
 
-A BED file generated by the *uORF Annotator* contains all uORFs affected by variants that alter the uORF length. The BED file contains one entry for each affected uORF, and one entry for each variant-uORF combination that leads to changes in anticipated length of uORF product. Color legend:
+*uORF Annotator* generates two BED files with uORFs affected by variants that alter the uORF length (one file contains ATG uORFs and the other contains non-ATG-started uORFs). Both BED files contain two entries for each affected uORF: 
+1) initial uORF, its `name` field format: uORF_unique_number-gene_name|uORF_type|start_codon_type(ATG/non-AT), filled with black color; 
+2) resulting uORF after introduction of a variant,  its `name` field format: uORF_unique_number-gene_name|variant|variant_type|main_CDS_effect,  filled with different colors depending on the effect. 
+
+Color legend: 
 * Grey features - cases when the variant does not change the overlap between uORF and main CDS.
 * Orange features - cases when (a) uORF-truncating variant eliminates the existing overlap between uORF and main CDS; or (b) variant leads to the production of a chimeric protein product of the gene, possessing an extension at the N-terminus resulting from uORF translation
 * Red features - cases where variant leads to the appearance of a new overlapping segment between uORF and main gene CDS, with the two sequences translated in different frames.
 
+
 ## Supplementary data files
 
 This repository contains two additional files: