Bioinformatics Stack Exchange
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Human Genome Alignment and Variant Calling Benchmarks

I am doing a project that requires bench-marking the performance of computational tools for alignment and variant calling of human genome sequencing data. In particular I would like to establish benchmarks comparing the performance of GATK and…
Jon Deaton
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Which data is being used for violin plot?

Sorry I just got totally confused conceptually. If this is my raw count data Likely, Seurat divides each value by sum of the column afterward times by 10000. which gives so s1.1 s1.2 s1.3 s1.4 s1.5 DDB_G0267178…
Zizogolu
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Detecting differentially expressed genes with foldchange >= 2 and FDR < 0.05

I'm using edgeR for differential analysis. Using glmTreat function I'm detecting differentially expressed genes between Tumor and Normal. I have set the arguments like below: tr <- glmTreat(fit, contrast=contrast.matrix, lfc=2) tab2 <-…
stack_learner
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Input normalization in ChIP-seq

If I subtract input counts from ChIP counts (for every gene, since I have one peak per gene) I get negative values for most genes. This makes sense to me, because (as can be seen in the figure) input and IP have same sequencing depth but IP is very…
aerijman
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2 answers

Download proteomes from NCBI based only on binomial names

I'm trying to download around 2000 proteomes from NCBI, but all I have is the genus and species e.g: lophodermium_seditiosum trichoderma_harzianum Does anyone know a good way of doing this in script form? My code at the moment is: from Bio import…
Biomage
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How do I estimate branch length of a maximum parsimony phylogeny in R?

I am trying to estimate a phylogenetic tree in R with ape and phangorn. With pratchet() and optim.parsimony(), I can estimate a phylogenetic tree, but branch lengths are not estimated. Is there a way to estimate a phylogeny with branch lengths with…
Namenlos
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determine if ChIP-seq peaks are broad or narrow

Is there a method to determine if the peaks are broad or narrow? ENCODE provides some guidelines: Although those cover common histone marks, there are many others. If you are using one of the ones that are not listed, is there a way to determine…
burger
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Can you query the RCSB PDB API with a ligand and return the IDs of all entries in which it appears as a free ligand?

If you're looking at the entry for a ligand, for example, adenosine, there's a link on the webpage to entries for which this entry exists as a free ligand. However, I want to access this via the API and can't seem to find docs/info on how to do…
AgTarlú
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Mapping a list of cells in seurat featureplot

I have 209 cells, I clustered them by Seurat to 4 clusters. By Featureplot I am able to track a gene in clusters: Higher color shows higher expression. Now, for some genes I want to highlight some cells in Featureplot so that apart from yellow or…
Zizogolu
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Disk space error while aligning reads using STAR

Hi am trying to align RNA-seq reads using STAR through following commands, STAR --runMode alignReads --runThreadN 26 --outSAMtype BAM SortedByCoordinate Unsorted --sjdbOverhang 100 --genomeDir wheat --readFilesIn G3_cleaned_R1.fastq…
Ammar Sabir Cheema
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Issues installing Dendropy

I want to perform phylogenetic analysis using Dendropy. I have installed dendropy using command sudo pip install -U dendropy but when I import it in python3.5.1 it gives followinng error: > python3 Python 3.5.1 |Anaconda 2.5.0 (64-bit)|…
Ammar Sabir Cheema
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Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms

I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms. Specifically, I'd like to determine the rough location of side-chain hydrogens in glycine…
Jonathon Byrd
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Is there any tools that can generating FBA model from genome sequences or proteome sequences?

Suppose I have all sequences of genes or proteins of certain species, are there any free tools I can use to generate a flux balance analysis model out of them? What I was thinking is more like to annotate all the enzymes based on some annotation…
LifeWorks
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How do I find a list of PDB structures bound to a peptide inhibitor or peptide-like inhibitor?

I looked up existing databases but ones like iPPI-DB or enter link description here either provide non-peptide inhibitors or only sequences. I need structures of proteins bound to other proteins, the latter of which is an inhibitor of the former,…
blehblehblecksheep
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Difference between copy number neutral reads and active reads

In this paper, the authors talk about copy number neutral reads (as reads that equally represent parental chromosomes) and active reads (as reads from only one parent chromosome): We reasoned that the reads mapped into a genomic window can be…
wrong_path
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