User: Alejandro Jimenez Sanchez

Reputation:
120
Status:
Trusted
Location:
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
Website:
http://miller-lab.org/
Last seen:
4 weeks ago
Joined:
3 years 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 >
0
votes
0
answers
637
views
0
answers
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 5 months ago by Alejandro Jimenez Sanchez120
0
votes
1
answer
385
views
1
answers
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 7 months ago by Alejandro Jimenez Sanchez120
0
votes
1
answer
385
views
1
answer
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 ...
0
votes
0
answers
307
views
0
answers
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 9 months ago by Alejandro Jimenez Sanchez120
0
votes
0
answers
743
views
0
answers
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 9 months ago by Alejandro Jimenez Sanchez120
0
votes
0
answers
743
views
0
answers
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 10 months ago by Alejandro Jimenez Sanchez120
0
votes
0
answers
743
views
0
answers
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 11 months ago by Alejandro Jimenez Sanchez120
0
votes
0
answers
743
views
0
answers
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 11 months ago by Alejandro Jimenez Sanchez120
7
votes
4
answers
1.2k
views
11 follow
4
answers
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 11 months ago by Alejandro Jimenez Sanchez120 • updated 4 months ago by sutturka120
0
votes
1
answer
338
views
1
answers
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 12 months ago by Alejandro Jimenez Sanchez120

Latest awards to Alejandro Jimenez Sanchez

Great Question 5 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 5 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 10 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?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Install ABSOLUTE Error
Popular Question 14 months ago, created a question with more than 1,000 views. For How to run multiple jobs with GNU parallel with multiple arguments?
Scholar 15 months ago, created an answer that has been accepted. For A: Install ABSOLUTE Error
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 ABSOLUTE to estimate tumour purity from WES data
Student 2.2 years ago, asked a question with at least 3 up-votes. For Protein database for TCGA MAF files
Supporter 2.3 years ago, voted at least 25 times.
Autobiographer 3.0 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1559 users visited in the last hour