User: Alejandro Jimenez Sanchez

Reputation:
120
Status:
Trusted
Location:
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
Website:
http://miller-lab.org/
Twitter:
AlejandroJS1407
Scholar ID:
Google Scholar Page
Last seen:
4 months, 3 weeks ago
Joined:
4 years ago
Email:
a***********************@cruk.cam.ac.uk

PhD candidate working on cancer genomics, tumour microenvironment, and heterogeneity.

Posts by Alejandro Jimenez Sanchez

<prev • 38 results • page 1 of 4 • next >
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vcf2maf not generating `t_depth t_ref_count t_alt_count` columns in MAF file
... I am using vcf2maf to convert VCF files into MAF files, however the columns `t_depth t_ref_count t_alt_count` are empty for some new VCF files I just got, but for previous ones I do get those columns filled. I haven't managed to figure out why the new VCFs are not giving me the `t_depth t_ref_count ...
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Comment: C: how to correct gene expression based on tumor purity
... Hi have you found an answer to this? For differential expression analysis using RNAseq data, it seems the package DESeq2 has a function that allows you to correct for purity estimates. See this paper: https://www.nature.com/articles/ncomms9971 ...
written 17 months ago by Alejandro Jimenez Sanchez120
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Comment: C: Processing Whole Genome Sequencing data (shallow) and call Copy Number Variation
... It is for copy number variations in tumour tissues, so germline changes would be removed. ...
written 19 months ago by Alejandro Jimenez Sanchez120
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Processing Whole Genome Sequencing data (shallow) and call Copy Number Variations
... Dear all, We are proposing a project where we want to perform shallow Whole Genome Sequencing (<1x) on DNA obtained from tumour FFPE human samples. I have worked before with Whole Exome Sequencing and I have called SNVs and so on, but I haven't worked with WGS yet. Does anyone know of any good ...
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Hyperbolic significance threshold for volcano plot
... Hi, I was wondering if anyone has an idea of how to generate an "statistically" meaningful hyperbolic function that could be used as significance threshold for volcanos plots. I have seen examples [here][1] and [here][2] in proteomics, and a colleague has the method for t-test in his [PhD thesis][ ...
volcanoplot written 21 months ago by Alejandro Jimenez Sanchez120
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Comment: C: ABSOLUTE MAF error
... Hi, With human samples everything ran smoothly. Maybe if you want, send me the first ~ 50 rows of your MAF and I can try to run it with my script... ...
written 21 months ago by Alejandro Jimenez Sanchez120
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Comment: C: ABSOLUTE MAF error
... I added `t_vaf` and make sure that the chromosome names were the same between the MAF and the seg file. I should say that the data I am trying to analyse is mouse data, and when I run human data I don't have the problem. I know Absolute was developed for human data, but I was giving it a try. I want ...
written 22 months ago by Alejandro Jimenez Sanchez120
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Comment: C: ABSOLUTE MAF error
... Thanks for your comment. Indeed the original MAF file had it with uppercase, but when I run it I get the following error: Error in `[.data.frame`(maf, , "Start_position") : undefined columns selected Thus, I changed Start_Position to Start_position, the same for End_position. Then I get t ...
written 22 months ago by Alejandro Jimenez Sanchez120
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ABSOLUTE MAF error
... I am running ABSOLUTE 1.0.6 in R 3.4.0 When I do: RunAbsolute(seg.dat.fn, sigma.p, max.sigma.h, min.ploidy, max.ploidy, primary.disease, platform, sample.name, results.dir, max.as.seg.count, max.non.clonal, max.neg.genome, copy_num_type, maf.fn, min.mut.af, output.fn.base=NULL, verbose=TRUE) ...
maf absolute written 23 months ago by Alejandro Jimenez Sanchez120 • updated 10 months ago by kmvaldez210
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Download SAM/BAM files from SRA takes ages!!!
... Dear all, I have tried sam-dump SRR3330607 | samtools view -bS - > 42RF.bam and sam-dump SRR3330607 > SRR3330607.sam And it is taking hours to download, is there a more efficient way to download these files from SRA? I want to use the bam files, and I have many other samples to ...
sra bam written 23 months ago by Alejandro Jimenez Sanchez120 • updated 7 months ago by shengwei30

Latest awards to Alejandro Jimenez Sanchez

Popular Question 8 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 12 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 12 months ago, created a question with more than 1,000 views. For TCGA Mutation Annotation Files (MAFs) with ref_context column
Popular Question 12 months ago, created a question with more than 1,000 views. For Data repository for Whole Exome Sequencing
Great Question 17 months ago, created a question with more than 5,000 views. For How to run multiple jobs with GNU parallel with multiple arguments?
Popular Question 17 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 22 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 2.0 years ago, created a question with more than 1,000 views. For How to run multiple jobs with GNU parallel with multiple arguments?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Install ABSOLUTE Error
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to run multiple jobs with GNU parallel with multiple arguments?
Scholar 2.3 years ago, created an answer that has been accepted. For A: Install ABSOLUTE Error
Popular Question 2.4 years ago, created a question with more than 1,000 views. For How to run multiple jobs with GNU parallel with multiple arguments?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For ABSOLUTE to estimate tumour purity from WES data
Student 3.1 years ago, asked a question with at least 3 up-votes. For Protein database for TCGA MAF files
Supporter 3.2 years ago, voted at least 25 times.
Autobiographer 4.0 years ago, has more than 80 characters in the information field of the user's profile.

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