User: Alejandro Jimenez Sanchez

Reputation:
90
Status:
Trusted
Location:
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
Website:
http://miller-lab.org/
Last seen:
1 week, 1 day ago
Joined:
1 year, 11 months ago
Email:
a***********************@cruk.cam.ac.uk

I am a graduate student interested in cancer research both from the dry and wet lab. Currently, I am working on a cancer immunoediting model.

Posts by Alejandro Jimenez Sanchez

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Protein database for TCGA MAF files
... Hi, You can find the code and example files in our GitHub rep here: [https://github.com/cansysbio/immunogenomics/tree/neoepitopes][1] I should emphasise that the code and the example files are only for example purposes, if you try to run the code with the example files it won't work because you ne ...
written 24 days ago by Alejandro Jimenez Sanchez90
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Comment: C: Protein database for TCGA MAF files
... You can download from [ensembl][1] for example. If you used a different reference genome, you just have to move to the parent directories and search on the correct genome. I'm not sure the script would work as it is right now, since I have other functions linked etc. But let me check and I'll share ...
written 25 days ago by Alejandro Jimenez Sanchez90
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Comment: C: Protein database for TCGA MAF files
... Hi, I used the proteome file that corresponds to the GRCh build that I used. I wrote a script that checks that the wild type amino acid in the position of the mutation is the same as the one annotated in the MAF. It worked very well. Also there's a new tool called [MuPeXI][1]. You only need to inpu ...
written 25 days ago by Alejandro Jimenez Sanchez90
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Answer: A: Install ABSOLUTE Error
... I've found the solution. I downloaded again the tar.gz file and installed the package from source by doing: R CMD INSTALL ABSOLUTE_1.0.6.tar.gz In the directory where the tar.gz file was located. Then, doing: library(ABSOLUTE) Works. I'll leave this here in case someone needs it in th ...
written 11 weeks ago by Alejandro Jimenez Sanchez90
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Install ABSOLUTE Error
... Hello, A while ago I ran [ABSOLUTE][1] and I have the script I used. I want to run it again but when I do: library(ABSOLUTE) I get: Error in library(ABSOLUTE) : there is no package called ‘ABSOLUTE’ If I do: install.packages("ABSOLUTE", lib="/Library/Frameworks/R.framework/Versio ...
absolute R package written 11 weeks ago by Alejandro Jimenez Sanchez90
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Data repository for Whole Exome Sequencing
... Hi, I was wondering if there is any data repository like [GEO][1] for Whole Exome Sequencing data. Thanks for your help. Alejandro UPDATE If anyone has the same question, it was quite easy to upload the bam files to the [SRA database][2]. Thanks for the suggestions! [1]: https://www.ncbi.nl ...
geo database wes written 5 months ago by Alejandro Jimenez Sanchez90
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Answer: A: Where Can I Download All Exons Of The Human Genome In Fasta Format (One Big File
... If anyone is looking for the same but for GRCh37 [here][1] is the link. [1]: http://grch37.ensembl.org/biomart/martview/35a76216fa3fb9762f17c7c2cf5aecbf ...
written 9 months ago by Alejandro Jimenez Sanchez90
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Answer: A: Hypergeometric Test On Gene Set
... I think method 1 is the correct one, because. Method 1 gives the same result as this site: https://www.geneprof.org/GeneProf/tools/hypergeometric.jsp Method 2 gives a different result. ...
written 13 months ago by Alejandro Jimenez Sanchez90
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Is it possible to include all possible gene transcripts affected by a mutations using vcf2maf?
... To convert VCFs to MAFs I use the very well documented tool [vcf2maf][1]. In the introduction it says: > To convert a VCF into a MAF, each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. This selection of a single effect per variant, is often s ...
vcf2maf written 13 months ago by Alejandro Jimenez Sanchez90
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Comment: C: How to run multiple jobs with GNU parallel with multiple arguments?
... The --verbose output is: ./script.sh argA argB1 argC ./file.txt ./script.sh argA argB2 argC ./file.txt I don't understand why it works only for the first one, while when it comes the second line ./script.sh gives the error `predict_binding.py: error: incorrect number of arguments` I am us ...
written 14 months ago by Alejandro Jimenez Sanchez90

Latest awards to Alejandro Jimenez Sanchez

Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Install ABSOLUTE Error
Popular Question 8 weeks ago, created a question with more than 1,000 views. For How to run multiple jobs with GNU parallel with multiple arguments?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Install ABSOLUTE Error
Popular Question 4 months ago, created a question with more than 1,000 views. For How to run multiple jobs with GNU parallel with multiple arguments?
Popular Question 9 months ago, created a question with more than 1,000 views. For ABSOLUTE to estimate tumour purity from WES data
Student 13 months ago, asked a question with at least 3 up-votes. For Protein database for TCGA MAF files
Supporter 14 months ago, voted at least 25 times.
Autobiographer 23 months ago, has more than 80 characters in the information field of the user's profile.

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