# All Questions

2,171 questions
Filter by
Sorted by
Tagged with
16 views

### How can I translate infix to mathml using the python interface to libsbml?

Assume I have an infix expression such as k1*s1, how do I use libsbml to translate this expression to mathml using the python interface?
18 views

### fold-change range

I am working on meta-analysing of microarray data of normal and breast cancer tissues. When I run the combatch for removing the BatchEffect I get these results: ...
35 views

### Statistical test design question

I have condition as such mouse liver and spleen data. So in liver I have WT (Wild Type) and KO (knock out) as well as in spleen WT (Wild Type) and KO (knock out). I have to compare the parasite load ...
19 views

### rentrez to retrieve NIH files

I'm trying to use rentrez package to retrieve NIH files, and ran the following code (I followed what was on the rentrez tutorial): ...
24 views

### A problem in meta-analyzing microarrays

I am working on meta-analysing of microarray data of normal and breast cancer tissues. When I run the combatch, I encounter this error: ...
37 views

### Alternative to enrichR for enrichment analysis?

I have been using EdgeR to perform differential expression analysis on bulk RNASeq data sets. This analysis gives me an output dataframe that has a list of all the genes, ranked by the their adjP ...
30 views

### How to find novel transcripts using GFFcompare?

I am trying to find novel transcripts from an RNA-seq database. Based on the advice I got, it seemed that using Stringtie for transcript assembly is a good way to go, and it supports novel transcript ...
25 views

### How to install UnThermo R package?

There is this R package that apparently can be used to convert Thermo Fisher RAW instrument files. But there is no description provided on how to install it. Does anyone know how to install it? https:...
49 views

### Which statistical test to use for comparing two groups?

I have data for 396 transcriptional factors (TF), where I have calculated the number of Transcriptional targets for each transcriptional factor present between the two groups: Group-I(G-I): where co-...
30 views

### How should I deal with segmental duplications when aligning NGS reads to a reference genome?

This is a follow-up of my other question. I have been having trouble calling variants in the human SMN1 and SMN2 genes, because the human genome has a large segmental duplication there and these two ...
52 views

### Proteomics data Vs Transcriptomics data?

I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...
35 views

### What are the right parameters to trim a small RNA transcriptome with trimmomatic?

I'm having some problems with finding the right parameters to trim my small RNA Illumina reads (51 nt long) with Trimmomatic. Before trimming, one of the samples (21M reads) looks like this: So for ...
13 views

### How can I figure out the cluster that low express in a specific gene in Seurat?

I'm following the standard protocol of Seurat so far and I know that Seurat can display the cluster that high express in a specific gene, however, I want to display the cluster that low express in a ...
25 views

### for loop cutadapt for files on a single directory

I have a bigfolder where i have a lot of fastq.gz files and I want to remove the adapters from all of them. I am trying then the following loop: ...
23 views

### How to select only RNA with Hetero atoms from pdb file with python?

I'm trying to separate RNA from protein in a complex protein/RNA PDB file and I want all RNA info with the hetero atoms in between the bases BUT without H20 etc. In short I want RNA part of pdb file ...
63 views

### How can I locate duplicated regions in a sequence?

I am facing an issue when trying to align short reads against a region in human chr5. The two Sensory Motor Neuron genes, (SMN1 and SMN2) are almost 100% identical and this causes the aligner to fail ...
17 views

### How to interprete PlasmidSeeker results concerning plasmids?

I've been interested in plasmid detection in bacterial genomes. I tried plasmidfinder and this software found only one plasmid in each of my two bacterial genomes. I was dubious about these results, ...
30 views

### DoHeatmap Hierarchical Clustering Seurat

I have a list of genes that I'd like to visualize using the DoHeatmap function in Seurat. However, the output of the heatmap does not result in hierarchical clustering and therefore makes it very ...
27 views

### ChrQ definition

What is ChrQ? I assume it then means chromosme Q or something like that yet when I google for it I get very weird answers, but as I saw that a couple times when looking on freebayes pipelines manuals ...
43 views

### Pandas automatically rounds GWAS P-value

I am working with a specific GWAS. If I were to run this on the command line grep <rs_id_of_interest> GWAS.txt I would see the GWAS p-value to be on the ...
38 views

### Using install.packages with conda-managed R

I have R installed and managed by conda (miniconda) on my MacBook Pro. The version of R I use most frequently (3.5.1) is installed on the base environment and I have other version-specific ...
22 views

### Annotating conserved protein domains in bacterial assemblies

I understand the basic principles under which RPS-BLAST operates: search a protein (rpsblast) or nucleotide (rpstblastn) query ...
9 views

### return cds from a protein fasta based on gene ID in unix?

I'm trying to retrieve cds sequences for given genes. Which requires taking a list of genes gene27 gene28 Retrieving their Gene ID (LOC##) and using faa to ...
10 views

### Cluster is split in 2-3 locations on tsne plot - Suerat

I am running a single cell dataset (count data - exon) through Seurat. After running tsne I see a cluster (13) split in 3 different locations on the plot. Here are the commands I am running: ...
40 views

### How can I transform a mapped BAM file into an unmapped BAM file?

In order to use MergeBamAlignment (Picard), I need an unmapped BAM file and a mapped BAM file. I have two mapped BAM files: one with reads mapped to the reference I want but without metadata such as ...
27 views

### How to run 'join' command for multiple files (of 2 types) in a folder

I have two types of files for a gene in a folder File 1: FOS.tf.txt ABL2 ACTN4 ADGRE5 ADIPOR2 ADRB2 ERCC4 EZR FAS FMO4 File 2: FOS.tt.txt ...
70 views

### How to combine multiple files into one file?

I have multiple files (n=86000) with one column each and I want to combine them all into one file with 86000 columns. I tried the following command ...
27 views

### How to output only the overlapping region of two files?

I have two files of genomic coordinates. I am trying to output only the overlapping region of fileA if it intersects with fileB. Not the original fileA coordinates. fileA ...
40 views

### Trying to change the element of a specific coordinate in a dataframe in r

So I am analyzing RNA sequence data, and putting my data into an excel spreadsheet. The way I am doing that is taking lists, and converting them to data frames, that I then cbind.data.frame together ...
43 views

### Subset a protein fasta based on sequence length?

I have a strange protein fasta file. There are several entries for the same gene and I need to extract the entry with the longest width. ...
36 views

...
103 views

### Convert BAM to properly paired FASTQ files

I thought I had figured this one out. But apparently not. I need to convert a BAM file of paired-end alignments to two FASTQ files of paired reads to realign them, with a twist: I only want reads ...
62 views

### How are UMIs used to dedupulicate in Drop-seq tools?

The module DigitalExpression which is part of the popular Drop-seq tools digitally count gene transcripts. The manual is not very clear on how exactly it resolves ...
52 views

### Why is 42 the seed used in RunPCA() in Seurat?

The RunPCA() in Seurat 3.0 function has seed.use=42 by default. How does one choose a seed number? Is this chosen simply because ...
53 views

### What do the read colors in IGV mean?

I was looking at a bam file in the IGV viewer and saw: What do the different read colors mean? Why is one read a light blue color, another green, another aquamarine (?), another purple and another ...
13 views

### Is there a computational method/method/way to predict if a cell population in a tissue immigrated or is enriched locally?

I have single cell data which I have analysed for differential expression. In my experiment, I subjected two groups of mice (a control and a treatment group) to treatment that will lead to the ...
42 views

### Error while calling bcftools mpileup - Failed to open -: unknown file type

I have sequenced a bacterial genome with a GridIon from ONT. Basically what I want to check is whether or not trimming 50 bps at the beginning of the reads will improve alignment against the reference ...
19 views

### Error: package or namespace load failed for 'ChIPseeker'

How do I solve the problem of loading the bioconductor Chipseeker package? I have installed in the following way and I having an error while loading it and I do not know why. ...
17 views

### query specific chunk file using python [closed]

I'm doing a project using mongodb and python. In my project have files to store, but that file are greater than 16MB. For that I used gridfs to solve my inserting issue. Now I have a requirement to ...
27 views

### How can I correctly get 3D scatter plot for micro-array pheno data in R [updated]?

I intend to see data points distribution (each reows) within labeled groups (different batchs such as 1,2,3, and so on) in 3D scatter plot, because I want to see the distribution of the data points ...
76 views

### Raw Data frame manipulation in python

Using python 3 I need to process qPCR sequencing raw data outputs by searching for the first occurrence of a user defined string and then making a new data frame using all lines after that string. I ...
45 views

### Is there a standard tool used to convert a VCF to a BEDPE?

Many popular SV callers output a VCF. Unfortunately, there isn't a unified system at the present to label events with the same notation. However, is there a standard method for converting these VCFs ...
8 views

### How to integrate the transcriptomics data with kinetic metabolic models?

I have created a convenience kinetics model. Now, I want to integrate the transcriptomic data with my convenience kinetics* model for altering/weighing the kinetic parameter values. I read some ...
35 views

### Reducing a string to a certain amount of the first characters in R

So I have a list of several thousand RNA transcripts, and I am trying to find out how they are spliced. Right now I am running matchLRpatterns() from the Biostrings ...
78 views

### Strange p-value histogram for differential gene expression analysis

I'm trying to perform pretty standard differential expression analysis using RNA-seq data. I've used Kallisto to perform RNA quantification and am using Sleuth to perform the differential expression ...
35 views

### how to merge two fasta based on full fasta header and remove the duplicate

I am wondering if anyone can help to merge two fasta file based on the full header as initially gene ID may be similar in some of the sequences and to remove the duplicate entry based on full fasta ...
25 views

### How to create Seurat object while RNA expression and ADT combined into one matrix

I got an input matrix which RNA expression and ADT capture are combined into one file. I loaded the file into Seurat successfully, however, when I tried to create Seurat object, it threw out an error ...
48 views

### Produce a single sequential FASTA sequence out of BAM

I'm having problems properly looking for a solution because I'm a layman in Bioinformatics not familiar with the terminology. I'm hoping you can nudge me in the right direction, please! Thank you very ...