Difference between revisions of "Fabry:Mapping point mutations/Journal"
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R CMD BATCH [https://www.dropbox.com/s/l7e15x2kepcwzee/snp_distr.R.txt snp_distr.R] |
R CMD BATCH [https://www.dropbox.com/s/l7e15x2kepcwzee/snp_distr.R.txt snp_distr.R] |
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| − | Afterwards we tried to vizualise disease and non-disease causing point mutations in one plot with [https://www.dropbox.com/s/y9b0j1ozofn9rku/Hotspots_all.R.txt Hotspots_all.R]. We needed R tables of all databases for this, so some preparation had to be done with [https://www.dropbox.com/s/s8uvdog5n1q5kva/readHGMDforR.pl.txt readHGMDforR.pl] and [https://www.dropbox.com/s/60rn67orhh9t29j/readdbSNPforR.pl.txt readdbSNPforR.pl] |
+ | Afterwards we tried to vizualise disease and non-disease causing point mutations in one plot with [https://www.dropbox.com/s/y9b0j1ozofn9rku/Hotspots_all.R.txt Hotspots_all.R]. We needed R tables of all databases for this, so some preparation had to be done with [https://www.dropbox.com/s/s8uvdog5n1q5kva/readHGMDforR.pl.txt readHGMDforR.pl] (input [https://www.dropbox.com/s/i2vvunjz1kbxmfy/hgmd_snps.txt hgmd_snps.txt]) and [https://www.dropbox.com/s/60rn67orhh9t29j/readdbSNPforR.pl.txt readdbSNPforR.pl] (input [https://www.dropbox.com/s/i96c1wscdxqyb01/dbSNP_snps.txt dbSNP_snps.txt]) |
perl [https://www.dropbox.com/s/s8uvdog5n1q5kva/readHGMDforR.pl.txt readHGMDforR.pl] |
perl [https://www.dropbox.com/s/s8uvdog5n1q5kva/readHGMDforR.pl.txt readHGMDforR.pl] |
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Revision as of 08:07, 10 June 2012
Fabry Disease » Mapping point mutations » Journal
OMIM
In this database we searched for the gene GLA and downloaded the Table View table of the Allelic Variants (Allelic_variants.txt), which can be found in the Table of Contents. This table was parsed with the perl scripts readOMIM.pl and Omim2table.pl, which created all the output we needed for creation of the tables and statistics.
perl readOMIM.pl perl Omim2table.pl > omim.wiki
SNPedia
Since there is no special site for the gene GLA, we performed a query with the search term "Gene=GLA". These dbSNP identifiers were downloaded and mapped onto a list of all informations on all identifiers (201) found, when searching for ""snp"[SNP_CLASS] AND GLA[GENE] AND "human"[ORGN]" in the dbSNP (Flat File display). This was done with the perl script parse_dbSNP.pl, which needed the input files snp_result.txt and rsnumber.txt. A wiki table was created with SNPedia2table.pl.
perl parse_dbSNP.pl perl SNPedia2table.pl > SNPedia.wiki
SNPdbe
The textfile containing all informations gathered in SNPdbe (snps.txt) was downloaded after searching for the gene identifier "NP_000160" in the organism "human" (see). The textfile was parsed with the perl scripts readSNPdbe.pl and SNPdbe2table.pl and vizualised with the R script Hotspots_SNPdbe.R. For now, a SNP was considered disease causing if there was a disease listed, if it was a "N/A" it was assigned "non-disease".
perl readSNPdbe.pl perl SNPdbe2table.pl > SNPdbe.wiki R CMD BATCH Hotspots_SNPdbe.R
Mapping
First of all, we created the plots showing the distribution of SNPs along the sequence of the gene GLA with the R Script snp_distr.R. For this we prepared the data with map.pl
perl map.pl R CMD BATCH snp_distr.R
Afterwards we tried to vizualise disease and non-disease causing point mutations in one plot with Hotspots_all.R. We needed R tables of all databases for this, so some preparation had to be done with readHGMDforR.pl (input hgmd_snps.txt) and readdbSNPforR.pl (input dbSNP_snps.txt)
perl readHGMDforR.pl perl readdbSNPforR.pl R CMD BATCH Hotspots_all.R
