Kevin Meza Landeros / MonogenicDiseases

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Kevin Meza Landeros
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1 -# MONOGENIC DISEASES 1 +1# MONOGENIC DISEASES
2 ## Human Genomics Project 2 ## Human Genomics Project
3 3
4 Team: 4 Team:
...@@ -11,35 +11,42 @@ Here we display all the data and scripts used in order to answer one of the most ...@@ -11,35 +11,42 @@ Here we display all the data and scripts used in order to answer one of the most
11 **Which is the proportion of diseases that are caused due to afections in coding and non coding regions?** 11 **Which is the proportion of diseases that are caused due to afections in coding and non coding regions?**
12 12
13 ## Folder content 13 ## Folder content
14 -- *alignments* 14 +- Grsphs
15 + Has plots that show the proportion of coding and non-coding sequences of Monogenic Diseases.
16 + - Grafica1.png
17 + - Grafica2.png
18 +- <ins>*alignments*</ins>
15 Contains the resultant files of aligning the secuences from genes of interest (that cause a monogenis disease) to the human genome. 19 Contains the resultant files of aligning the secuences from genes of interest (that cause a monogenis disease) to the human genome.
16 - sequences_aligned_A.bam 20 - sequences_aligned_A.bam
17 - sequences_aligned_A.sam 21 - sequences_aligned_A.sam
18 - sequences_aligned_A_sort.bam 22 - sequences_aligned_A_sort.bam
19 -- *data* 23 +- <ins>*data*</ins>
20 - *DISEASES DB* 24 - *DISEASES DB*
21 - Stores one of the databases use for the project and a file that has all the information of the monogenic diseases contained within it. 25 + Stores one of the databases use for the project, a file that has all the information of the monogenic diseases contained within it.
22 - human_disease_textmining_full.tsv 26 - human_disease_textmining_full.tsv
23 - - merge_list_monogenic_diseases.tsv 27 + - merge_list_monogenic_diseases.tsv (list of genes form "merge_monogenic_diseases.tsv")
24 - merge_monogenic_diseases.tsv 28 - merge_monogenic_diseases.tsv
25 - *Ensembl* 29 - *Ensembl*
26 - Harbors information about human genes. 30 + Harbors the following information about human genes: Gene start (bp); Gene end (bp); Gene type; Gene name; Strand; Protein stable ID
27 - mart_export_v2.txt 31 - mart_export_v2.txt
28 - *Homo_sapiens* 32 - *Homo_sapiens*
29 Includes human genome sequence and it's annotation. 33 Includes human genome sequence and it's annotation.
30 - - Homo_sapiens.GRCh38.100.gff3.gz 34 + - Homo_sapiens.GRCh38.100.gff3.gz (annotation)
31 - - Homo_sapiens.GRCh38.dna.alt.fa.gz 35 + - Homo_sapiens.GRCh38.dna.alt.fa.gz (sequence)
32 - *OMIM* 36 - *OMIM*
33 - Contains a file that has information about different heritable conditions, and another file has the information that corresponds to monogenic diseases. 37 + Contains a file that has information about different heritable conditions and that was was filtered to get what corresponds to monogenic diseases.
34 - - genemap2.txt
35 - gene_filtered_phenENS.txt 38 - gene_filtered_phenENS.txt
36 -- *scripts* 39 +- <ins>*scripts*</ins>
37 Has the scripts that were used through this project. 40 Has the scripts that were used through this project.
41 + - CambioCol.R
38 - ObtencionSecuencias.R 42 - ObtencionSecuencias.R
43 + - ObtenciondeAllData.R
39 - alineamiento.sh 44 - alineamiento.sh
40 - - get_monogenic_disease_data.sh 45 + - get_monogenic_disease_data_DISEASES.sh
46 + - get_monogenic_disease_data_OMIM.sh
47 + - mapeo.R
41 48
42 49
43 ## Results 50 ## Results
44 51
45 -![Biotipo de los genes que causan enfermedades Mendelianas.]( Graphs/Grafica1.png) 52 +![Biotipo de los genes que causan enfermedades Mendelianas.]( Graphs/Grafica2.png)
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