Scripts-Descriptions.md

@@ -4,20 +4,27 @@ Plant Computational Genomics Lab @ UConn
 The scripts used in the processing of the supporting genomic and transcriptomic data are available in the appropriate subdirectories of the [processing repository](https://gitlab.com/PlantGenomicsLab/annotationtool/tree/master/process). These are kept in groups based on processing step. [This page](https://gitlab.com/PlantGenomicsLab/annotationtool/wikis/Scripts-Descriptions) (here) is an atlas of script function, listed alphabetically by script name within each step category, which are listed sequentially.
 
 Table of Contents
-* [Gathering Data](#Gathering-Data)
-* [TSA Prep](#Preparing-TSA-Files)
+* [Gathering Data](#gathering-data)
+* [Assembly Filtering](#assembly-filtering)
+* [TSA Prep](#preparing-tsa-files)
+* [Softmasking Genome](#softmasking-genome)
+* [Genome Statistical Assessment](#genome-statistical-assessment)
+* [Preparing TSA Files](#preparing-tsa-files)
 
 
 #### Gathering Data
+The genomic and transcriptomic data used for the experiment was sourced from NCBI
 Name | Step | Purpose | Input | Expected Output | Notes
 ---- | ---- | ------- | ----- | --------------- | -----
 fetchSRA.sh | gather data |  Gather data from multiple NCBI SRRs (**S**equence **R**ead archive **R**un accessions) | Text file containing the specific SRR runs that you want to download | raw reads in .fastq format | the option `--split-files` in line 22 must be removed if gathered data is not paired
 validateSRA.sh | gather data |  Validates that the correct files have been downloaded from NCBI | Text file containing the specific SRR runs that you want to download | an output and error file confirming that all runs were downloaded correctly | 
 
+#### Assembly Filtering
 Name | Step | Purpose | Input | Expected Output | Notes
 ---- | ---- | ------- | ----- | --------------- | -----
 filtersubmit.sh | filter | run filterLen.py with the correct module and input settings to remove small scaffolds from genome assembly | genome assembly of interest | genome assembly excluding scaffolds < 500 bp | 
 
+#### Softmasking Genome
 Name | Step | Purpose | Input | Expected Output | Notes
 ---- | ---- | ------- | ----- | --------------- | -----
 repeatModeler.sh | mask | Use [RepeatModeler](http://www.repeatmasker.org/RepeatModeler/) to generate a de novo repeats library for a genome | filtered genome assembly in fasta format | repeats library suffixed conseni.fa.classified |   
@@ -25,15 +32,16 @@ concat.sh | mask | Concatenate all of the pieces of the split and softmasked gen
 repeatmasker.sh | mask | Use [RepeatMasker] to softmask the regions in the genome recognized as repetitive | a piece of the filtered genome, repeat library generated by [RepeatModeler](http://www.repeatmasker.org/RepeatModeler/) | softmasked piece of genome | 
 splitfasta.sh | mask | Reduce the running time for repeatmasker by splitting the genome into pieces | filtered genome in fasta format | multiple pieces of filtered genome | 
 
+#### Genome Statistical Assessment
 Name | Step | Purpose | Input | Expected Output | Notes
 ---- | ---- | ------- | ----- | --------------- | -----
 wholegenomebusco.sh | assembly stats | Use [BUSCO](https://busco.ezlab.org/) to assess genome completeness | Length-filtered/softmasked genome assembly & appropriate single-copy ortholog dataset | Genome completeness benchmark results including predicted genes, alignment results & statistics | 
 
-##### Preparing TSA Files
+#### Preparing TSA Files
 Name | Step | Purpose | Input | Expected Output | Notes
 ---- | ---- | ------- | ----- | --------------- | -----
 frameSelect.sh | TSA Prep | Uses [TransDecoder](https://github.com/TransDecoder/TransDecoder/wiki) to identify coding regions in the transcript assemblies and translate into peptide sequences | TSA fasta file | BED, GFF3, CDS (nt coding sequence) & peptide files representing recovered coding regions |  
-usearch.sh | TSA Prep | Uses [USearch v9.0](https://www.drive5.com/usearch/manual9/) to cluster multiple frame-selected TSAs (**T**ranscriptome **S**hotgun **A**ssembly) by sequence homology into a consensus transcriptome | A single fasta made of concatenated frame-selected TSAs | Clustered reference transcriptome | . 
+usearch.sh | TSA Prep | Uses [USearch v9.0](https://www.drive5.com/usearch/manual9/) to cluster multiple frame-selected TSAs (**T**ranscriptome **S**hotgun **A**ssembly) by sequence homology into a consensus transcriptome | A single fasta made of concatenated frame-selected TSAs | Clustered reference transcriptome |