User: inesdesantiago

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inesdesantiago
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Posts by inesdesantiago

<prev • 20 results • page 1 of 2 • next >
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Answer: A: TCGA immunotherapy treated melanoma data
... Hi I use this: # Get all metadata metadata_clean <- recount::all_metadata("tcga") # Get only SKCM project x <- metadata_clean[metadata_clean$gdc_cases.project.project_id == "TCGA-SKCM",] dim(x) [1] 473 271 Now you can see 14 patients with Ipilimumab and 1 with ni ...
written 6 weeks ago by inesdesantiago170
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Answer: A: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
... New tools for RNA-seq tumors: QuantiSeq http://icbi.i-med.ac.at/software/quantiseq/doc/index.html and DeMixT https://www.biorxiv.org/content/early/2017/10/14/146795 ...
written 2.4 years ago by inesdesantiago170
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Answer: A: Generating Mappability Files
... This is how I have done it: #download code and make mkdir Mappability_Map curl http://archive.gersteinlab.org/proj/PeakSeq/Mappability_Map/Code/Mappability_Map.tar.gz tar -zxvf Mappability_Map.tar.gz -C Mappability_Map make #download reference genome curl http://h ...
written 3.1 years ago by inesdesantiago170
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Answer: A: unite histone sites, DNAse, Chip-seq data from different cell types.
... The haploreg webtool from the Broad (http://www.broadinstitute.org/mammals/haploreg/haploreg.php) can give you some hints of the TFs that bind to those SNPs. It uses all ENCODE data and the output tells you what are the TFs and cell lines at each SNP. It also use predicted TFBS motifs and their scor ...
written 5.0 years ago by inesdesantiago170
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Answer: A: SNP calling on ChIP-seq data
... Hi. I did try that at some point, and compared to published genotypes (from ENCODE). Works ok as long as you don't have cancer genomes (for this one needs to use specific snp calling pipelines to deal with copy-number aberrations and tumor/normal mixtures).  But for normal genomes, I think it works ...
written 5.1 years ago by inesdesantiago170
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Comment: C: Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
... Use [Rsamtools pileup](https://seqqc.wordpress.com/2015/03/10/calculate-nucelotide-frequency-with-rsamtools-pileup/). ...
written 5.1 years ago by inesdesantiago170 • updated 5 months ago by RamRS26k
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Answer: A: Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
... You can use pileup and this function in R (with Rsamtools): pileupFreq <- function(pileupres) { nucleotides <- levels(pileupres$nucleotide) res <- split(pileupres, pileupres$seqnames) res <- lapply(res, function (x) {split(x, x$pos)}) res <- lapply(res, function (pos ...
written 5.1 years ago by inesdesantiago170
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Comment: C: Rsamtools::pileup gives inconsistent number of reads
... Thank you! it is solved by changing max_depth parameter within PileupParam() > pileup(bf, scanBamParam=param, pileupParam=PileupParam(max_depth=8000, min_mapq=0, min_base_quality=0))   seqnames       pos strand nucleotide count               which_label 1    chr10 100189138      +          A    ...
written 5.1 years ago by inesdesantiago170
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Answer: A: Rsamtools::pileup gives inconsistent number of reads
... Thank you! it is solved by changing max_depth parameter within PileupParam() > pileup(bf, scanBamParam=param, pileupParam=PileupParam(max_depth=8000, min_mapq=0, min_base_quality=0))   seqnames       pos strand nucleotide count               which_label 1    chr10 100189138      +          A    ...
written 5.1 years ago by inesdesantiago170
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Comment: A: Rsamtools::pileup gives inconsistent number of reads
... this is what samtools pileup command (from samtools) gives: samtools mpileup -B -sf $genome.fa -r chr10:100189138-100189138 test_aln75.bam [mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 chr10 100189138 A 300 G$.$g$,$G.g,G.g,G.g,G.g,G.g,G.g,G.g,G.g,G ...
written 5.1 years ago by inesdesantiago170

Latest awards to inesdesantiago

Great Question 2.4 years ago, created a question with more than 5,000 views. For How To Get A List Of All Correlated Snps (In Ld) With Another List Of Snps?
Epic Question 2.4 years ago, created a question with more than 10,000 views. For How To Get A List Of All Correlated Snps (In Ld) With Another List Of Snps?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: SNP calling on ChIP-seq data
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Rsamtools::pileup gives inconsistent number of reads
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How To Get A List Of All Correlated Snps (In Ld) With Another List Of Snps?
Great Question 3.0 years ago, created a question with more than 5,000 views. For How To Get A List Of All Correlated Snps (In Ld) With Another List Of Snps?
Scholar 5.1 years ago, created an answer that has been accepted. For A: Rsamtools::pileup gives inconsistent number of reads
Popular Question 5.8 years ago, created a question with more than 1,000 views. For How To Translate Encode Genotype Data From Aa/Ab/Bb To Standard A,T,G,C ?
Popular Question 5.8 years ago, created a question with more than 1,000 views. For How To Get A List Of All Correlated Snps (In Ld) With Another List Of Snps?

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