User: Alejandro Jimenez Sanchez

Reputation:
100
Status:
Trusted
Location:
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
Website:
http://miller-lab.org/
Last seen:
1 month, 1 week ago
Joined:
2 years, 8 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 • 37 results • page 1 of 4 • next >
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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 6 weeks ago by Alejandro Jimenez Sanchez100
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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 3 months ago by Alejandro Jimenez Sanchez100
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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 5 months ago by Alejandro Jimenez Sanchez100
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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 5 months ago by Alejandro Jimenez Sanchez100
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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 6 months ago by Alejandro Jimenez Sanchez100
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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 6 months ago by Alejandro Jimenez Sanchez100
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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 6 months ago by Alejandro Jimenez Sanchez100
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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 6 months ago by Alejandro Jimenez Sanchez100 • updated 6 months ago by ghostforever.shi20
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Comment: C: Mapping TCGA IDs
... Yes, I was looking into GDC portal, and I saw that each case file has both IDs if you keep clicking, but I haven't found a file with all cases having both IDs. Do you know if such a file exists? ...
written 8 months ago by Alejandro Jimenez Sanchez100

Latest awards to Alejandro Jimenez Sanchez

Popular Question 6 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 8 months ago, created a question with more than 1,000 views. For How to run multiple jobs with GNU parallel with multiple arguments?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Install ABSOLUTE Error
Popular Question 10 months ago, created a question with more than 1,000 views. For How to run multiple jobs with GNU parallel with multiple arguments?
Scholar 11 months ago, created an answer that has been accepted. For A: Install ABSOLUTE Error
Popular Question 13 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 18 months ago, created a question with more than 1,000 views. For ABSOLUTE to estimate tumour purity from WES data
Student 21 months ago, asked a question with at least 3 up-votes. For Protein database for TCGA MAF files
Supporter 23 months ago, voted at least 25 times.
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.

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