README.md


1# MONOGENIC DISEASES


Human Genomics Project

Team:


Garcia Flores Fernanda Renee
Meza Landeros Kevin Emmanuel
Schafer Juarez Badillo Alejandra Nicole
Zeferino Garcia Karla 


Here we display all the data and scripts used in order to answer one of the most relevant actual questions in the field of Human Health:

Which is the proportion of diseases that are caused due to afections in coding and non coding regions?  


Folder content


Grsphs
Has plots that show the proportion of coding and non-coding sequences of Monogenic Diseases.


Grafica1.png
Grafica2.png


alignments

Contains the resultant files of aligning the secuences from genes of interest (that cause a monogenis disease) to the human genome.


sequences_aligned_A.bam
sequences_aligned_A.sam
sequences_aligned_A_sort.bam


data


DISEASES DB

Stores one of the databases use for the project, a file that has all the information of the monogenic diseases contained within it.


human_disease_textmining_full.tsv 
merge_list_monogenic_diseases.tsv (list of genes form "merge_monogenic_diseases.tsv")
merge_monogenic_diseases.tsv


Ensembl

Harbors the following information about human genes: Gene start (bp); Gene end (bp); Gene type; Gene name; Strand; Protein stable ID


mart_export_v2.txt


Homo_sapiens

Includes human genome sequence and it's annotation.


Homo_sapiens.GRCh38.100.gff3.gz (annotation)
Homo_sapiens.GRCh38.dna.alt.fa.gz (sequence)


OMIM

Contains a file that has information about different heritable conditions and that was was filtered to get what corresponds to monogenic diseases.


gene_filtered_phenENS.txt 


scripts

Has the scripts that were used through this project.


CambioCol.R
ObtencionSecuencias.R
ObtenciondeAllData.R
alineamiento.sh
get_monogenic_disease_data_DISEASES.sh
get_monogenic_disease_data_OMIM.sh
mapeo.R


Results