This repository contains all the scripts required for the correct functioning of the master script of inmunoglobulin detection tool.

0. Variables confirmation
1. Make CDHIT reductions.
2. Align with CLUSTALW2 the RSS reductions.
3. Make BLAST analysis.
4. Convert BLAST m6 table to gff.
5. Extract scaffolds of interest.
6. Make EXONERATE analysis.
7. Clean vulgar format.
8. Make HMMER analysis for RSS.
9. Filter EXONERATE files for exons and genes hits.
10. Reduce to eliminate redundancy in filtered EXONERATE files.
11. Make overlap analysis to detect V segments with exon and SP
12. Make MINIPROT analysis.
13. Correct V segments and RSS-J coordinates.
14. Predict D segments based in founded RSS-D.

This script transforms blast format 6 (tabular with 11 columns) into a gff file, along with some filters.

blastm6_to_gff.py --file [FILE] --source [SOURCE] --bitscore [BITSCORE]

This script takes the vulgar format from the exonerate analysis and transforms the vulgar syntax into a table of condensed results.

vulgar_to_table.R --file [FILE]

This script transforms hmmer tbl format into a gff file.

hmmer_tbl_to_gff.py --file [FILE]

This script takes the filtered exonerate files (genes or exons) and perform a reduction of the overlaping sequences in order to reduce ambiguity produced from matches located at the same coordinates. The result is one genomic range per overlapping individual ranges.

gff_disambiguation.R --file [FILE]

This script takes two filtered files, the reduced exons and genes records from EXONERATE results. In order to detect if a V segment is a has its structural exon and its signal peptide, at least two exons need to be detected in each gene record. To do this, the number of exons per gene is counted and every gene that has two or more exons are annotated as genes, whereas genes with one or less associated exons are annotated as pseudogenes. Every record is numbered in a unique fashion to give each segment a unique name.

SCRIPTS/SUBSCRIPTS/predict_ighv_by_overlaps.R --query [FILE] --subject [FILE]

This script detect which RSS is locate nearby each V/J segment. This is achieved by increasing the coordinates of RSS segments in both the start and the end of the match, in order to try to make an artificial overlap with the nearby V/J segment

locate_nearby_rss.R -n [FILE] -t [FILE] -v [FILE] -r [INT] -m [STRING]

This script detects the probable location of true D segments. To do this, the reasoning was that true D segments would by flanked by D RSS signal in both 5' and 3' ends. Every genomic region comprising both ends that have less tha 50 bp lenght is considered as a potential true D segment.

predict_ighd_by_rss.R -f [FILE] -t [FILE]

The script uses many dependencies that could be annoying to install, test, and put the required locations. To prevent this, we designed a docker image in order to have a clean and ready-to-use environment to perform the genomic analysis using this script.

This are all the dependencies and the versions used in order to make the script to make all the analysis. Here are considered only the programs that could not be preinstalled in a new linux installation.