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Setting up MaxQuant parameters for processing proteomics data

This is a follow up to my previous question here. In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article "Diabetes causes marked inhibition of mitochondrial metabolism in…
Natasha
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GRanges coverage error with discordant reads

I mapped my fastq files from 4SU-seq experiment to human genome hg19 with bowtie 2 and got this results: 67716784 reads; of these: 67716784 (100.00%) were paired; of these: 29941143 (44.22%) aligned concordantly 0 times 33244334…
serbe204
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Grouping x-axis in scatter plot

I am trying to plot one scatter plot for each group, where each group has continous values in x-axis. Reference Data Gives continuous x-axis but all groups are combined. ggplot(data_for_plotting, aes(x = log10(Count), y =…
user98059
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Is there a generally accepted method used to impute missing DNA methylation data (probe beta-values)?

I'm looking at DNA methylation (DNAm) data such as TCGA (e.g., BRCA, KIRP, KIRC, etc.). Currently trying to build use my model to predict DNAm age on test sets, but many of the data sets are missing key probe values used in my clock/model. I have…
sumthymes
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Multiple file Python script

I am currently doing an analysis requiring a multiple-input script. I have a directory filled with 900+ samples. Each sample is comprised of two-files in a fastq format. This is an example of a sample: MIP_REV_BC_01_01A_S1_R1_001.fastq.gz…
Pranav Patel
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Processing proteomics data

[this question was also asked on BioStars] In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article "Diabetes causes marked inhibition of mitochondrial metabolism in pancreatic…
Natasha
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LRT test in deseq2 on multiple condition

I have some doubts when i'm running LRT This is my condition data-frame small subset dput(head(metadata,18)) structure(list(FAB = structure(c(1L, 1L, 1L, 1L, 6L, 2L, 6L, 4L, 3L, 5L, 7L, 3L, 2L, 7L, 6L, 2L, 6L, 2L), .Label = c("C", "M0", "M1",…
kcm
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Suggestion for python graphics library to plot aligned protein sequences

I'm working towards developing some visualization method for multiple protein sequences and subsequences using PYTHON. I want to show the alignment of many fragment sequences to the original sequences as well as the position of fragments and the…
The August
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What can be the reason of getting negative branches lengths after BEAST analysis?

BEAST2 is currently being used for tree reconstruction prior phylogeographic analysis. The sample size and loci are described below. I thought that BEAST/BEAST2 does not allow negative lengths of branches on prior distribution level so I was…
Vovin
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Missing ',' in line when Biopython reads a nexus tree

I want to edit a tree that I got from BEAST2 treeannotator in nexus-format. Usually I use the module Phylo from Biopython for such work but Phylo.read(r"filename.tree", "nexus") gave me the next…
Vovin
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Constructing Two Triangle Heatmaps in One Square

I'm looking to make a two, two range colour scheme heatmap where each range corresponds to a separate triangle in the heatmap square. I am looking for a relevant guide for this heatmap. Any recommended package/library or guides? Thanks!
raysteven
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Funcotator reference file error in GATK4

I am using a function called Funcotator (here) in GATK4. The code I am trying to run is: gatk Funcotator \ --variant chr21.vcf \ --reference hg38.fa.fai \ --ref-version hg38 \ --data-sources-path funcotator_dataSources.v1.2.20180329 \ --output…
Scott XU
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A question on Homer normalization

When using annotatePeaks.pl script from Homer software to create histograms, the output is normalized per bp per peak (on top of normalization to 10 million tags). What does it mean to normalize per bp per peak? Hypergeometric Optimization of Motif…
Sam
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3
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2 answers

Wrapping R scripts in WDL and run in docker

I am trying to run an R script as a task in WDL in a docker image. Since this is my first time working with these, I am stuck in something very simple (and in the initial stage) and am hoping somebody here can point me in the right direction. Here…
binn
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Detect mutation context in a read of a sam file

After sequencing (Illumina) of some DNA, I generated a sam file through alignment of a fastq file (using Bowtie2). Instead of using variant calling programs, I want to know the specific variances, compared to the reference genome, in each specific…
Annelisa
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