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2 views

Gene Regulatory Network (GRN) for given set of genes

I have somatic mutations from WES data and obtained a list of altered genes from mutations using ANNOVAR. My aim is to get a regulatory network for those genes where each edge in the network shows the ...
0
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2answers
37 views

Single cell RNAseq cell cluster (true cluster or sub cluster)

I am trying to run seurat on ~5000 sinngle cells. I am expecting minimum 15 cell types to be present in the data. I tried to runn it with multiple conditions;I can see there is 27 clusters; I believe ...
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2answers
38 views

Identifying nested/overlapping reading frames in nucleotide sequences

I'll start by saying I'm a total stranger to this field, so I'd love to be corrected if I misunderstood something along the way. I'm writing a python code to identify all the reading frames in a ...
0
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1answer
38 views

Is there an established method for comparing expression of groups of genes (gene sets)?

Basically the title. I have a figure in a paper where I show the log2(fold-change) (obtained with DESeq2) between two groups (based on genotype) for genes within a specific hallmark gene set, and a ...
1
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1answer
36 views

Truble to run a multiprocessing kmer count script

Hi there I have this code: ...
1
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2answers
29 views

Mapping statistics from bam file using bbtools and sambamba

Below are the statistics for RNA-seq mapped and unmapped paired-end reads to rice genome using reformat.sh from bbtools on bam files. It gives 77% mapped and 5% unmapped, what about the remaining 18% ...
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0answers
20 views

install bowtie2 from sources cannot find -ltbb

I am trying to install bowtie2 aligner from sources without the root access. Bowtie2 needs tbb package to be installed and it is recommended to install oneTBB. ...
0
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0answers
18 views

Truncated Chemical Names

Good Morning, I am currently researching treatment options for the Corona Virus from the CAS COVID-19 Antiviral Candidate Compounds Dataset available on the www.CAS.org. One issue we have run into is ...
3
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0answers
35 views

Using dssp after chain extraction

I have a list of PDB IDs with realtive chains that are to be extracted, and the run on dssp. For the single chain extraction I tried several methods, such as: ...
0
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0answers
17 views

How to correct the Effective Number of Codon

I am using the effective number of codons. I implemented its improved version proposed by S.Xiaoyang and colleagues (2012). Despite giving better results with respect to the original version proposed ...
0
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0answers
20 views

SeqFF for estimating freaction Error

I am beginning with bioinformatic genomic. I am very interested in NIPT. I use SeqFF.R package for estimating fetal fraction. I downloaded seqff.R package in https://obgyn.onlinelibrary.wiley.com/doi/...
0
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1answer
9 views

Running GSEA or comparable analysis with multiple variable interaction?

I am working with an RNA-seq dataset generated from a complex experimental design. Our main question is focused on the interaction between two variables, one (INJ) with two conditions (L,S) and the ...
2
votes
1answer
31 views

NCBI blast for exact match of a short sequence

I'm trying to Blast for exact matches to the sequence: 'ATTGNNNNGCAAACCA' in the human transcriptome using NCBI Blast on its 'refseq_rna' database. However, when I do a basic query I get "No ...
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0answers
13 views

For gene enrichment analysis, what are the difference among ORA, globaltest, and GSVA?

I am still new to bioinformatics, but I would like to know more about the algorithms for gene enrichment analysis. I studied for ORA, ...
1
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2answers
87 views

How to run Jupyter script on Slurm HPC

Now jupyter installed on the server and I am using below code to plot the rarefaction plot but I am still getting some error. could you please suggest how I can get rid of it? ...
2
votes
1answer
18 views

Targeted hybrid capture bam files showing reads outside target regions in my bed file

Sorry if this is a stupid question I am new to analysing targeted hybrid capture data. I am analysing my HTS data from a targeted hybrid capture enrichment method and subsequent sequencing on a ...
1
vote
1answer
33 views

What should be the numbers in the fastSTRUCTURE file?

The structure file for fastSTRUCTURE seem to be a table with rows and columns but the cells are all numbers, while my genotypes are simply bases. How could I know what I should insert there?
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0answers
36 views

summarising read group information from a .bam file

I have merged together 2 different .bam files in order to simulate sample contamination. So the reads can come from one of two samples, as shown by the read group info: ...
0
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0answers
10 views

Methods to analyze MeDIP-seq data

I have MeDIP-seq data. I have 6 groups with 15 replicates and a total of 90 human samples. I am trying to choose the best method to analyze them. I would highly appreciate if you can give me your ...
1
vote
1answer
23 views

Add segregating sites to branches of a tree

I'm trying to figure out how I would plot a tree with number of segregating sites on display on the branches I'm using acctran from phangorn to plot a parsimony tree (using phydat object from fasta ...
1
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0answers
19 views

Error while splitting PDBQT file

I am trying to split to a pdbqt file containing 178 compounds into individual pdbqt files. I have been using the Autodock Vina_split.exe file to split the multiple entry file however I keep running ...
1
vote
2answers
63 views

Interpreting GWAS results with different settings

I did a bunch of GWAS analysis (linear model without covariates) with applying different quality controls. How to choose the optimal settings when filtering for minor allele frequency (maf), Hardy-...
1
vote
1answer
25 views

predict the IC50 after using Schrodinger suite Glide tool for docking

How to predict the half-maximal inhibitory concentration (IC50) of my ligands. I'm currently using Schrodinger suite software and I don't know how to predict the IC50?
2
votes
1answer
50 views

Virus genome: protein inside another protein

The genome sequence for the GenBank virus JX869059.2 (a human betacoronavirus) contains, among others, two proteins: N protein (range 28566..29807) and Orf8b (range 28762..29100). The interval for ...
1
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1answer
14 views

How can I run the fdnadist command from the EMBOSS package?

My operating system is Mac OS X. I would like to compute DNA distances between different sequences. For this, the dnadist package from the Phylip software would be good but hard to automate. EMBOSS ...
0
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1answer
35 views

repophlan script to download bacterial genome

I am trying to donwload the microbial genome using the repophlan_get_microbes.py (https://github.com/SegataLab/repophlan) but now it is running more than 10 days and still not finished on slurm HPC. ...
1
vote
1answer
12 views

How to get the uniparc ids for all members of uniref cluster in batch request?

I currently use the 'UniProt website REST API' (example) to collect the UniParc IDs of all the members of the given cluster. Fetching each entry individually is very slow though, so I wanted to ask if ...
0
votes
1answer
59 views

Choosing Fisher's Exact or Binomial test for overrepresentation in PANTHER

The PANTHER website offers a tool to obtain the GO-based overrepresentation of a gene list (the analyzed list) versus a reference gene list. After entering both these lists, the tool asks to choose ...
0
votes
1answer
27 views

Get Dockerfile of a bioconda package

Bioconda packages have associated containers images. E.g. bioconductor-csaw has the image quay.io/biocontainers/bioconductor-csaw...
0
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0answers
12 views

Treat methylation as binary or continuous signal when detecting DMR?

Methylation level is usually measured as continuous value (M-value from 450K). However, DNA methylation is binary outcome in nature (methylated or not), and it is relatively easy to make the ...
1
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0answers
16 views

Finding original papers for gene annotations

I am wondering if there's a database to look up the annotation history of an arbitrary gene/ORF, with links to the primary literature for each step of the annotation. I have found that neither NCBI ...
0
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0answers
14 views

Extract Illumina reads that match with respect to their coordinates on the genome from fastq files

I want to use BPP to estimate divergence times and population sizes of a set of species. I have a vcf file with SNPs called from RADseq. The problem is that BPP uses the multi-species coalescent model ...
-3
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2answers
53 views

get sequences begining with TA [closed]

I have a fasta file and the sequences in them are arranged like this: ...
-1
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1answer
88 views

Find intersection among multiple columns and find the intersected elements [closed]

file input file ...
-2
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0answers
26 views

Python Multiprocessor pipeline

I have a variant calling pipeline containing multiple steps from different tools. Currently, I am working on Cray system. I have already ran the commands individually on single sample. Now, I want to ...
0
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0answers
26 views

Why do I get cytosine to guanine/adenine transitions in bisulphite treated sequences?

I got my sequencing results (bisulphite treated and non treated sequences of same species Allium cepa) and now I have to do analysis in Cymate online tool. I prepared all sequences as it is written in ...
0
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0answers
13 views

Predicting ATC codes at level 3 in python

I am trying to implement the algorithm implemented in this paper on Python. Basically it is a multi labeling algorithm to make out of sample prediction at level 1 of Anatomical Therapeutic Chemical (...
0
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1answer
34 views

BioJava - Protein to DNA

Using Biojava 5, I am trying to convert a sequence of Amino Acids to a Nucleotide sequence. Any idea how to do this?
0
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2answers
19 views

Installing HiC-Pro issues

I am setting up a HiChIPseq pipeline, but installing software necessary for the HiC side of things has been unbecoming. Both my PI and I have tried to install Hi-C Pro onto our Mac Pro that we use as ...
2
votes
2answers
93 views

How is the GT field in a VCF file defined?

As my question in SO was closed and asked to be posted in this forum, I am posting it here I am not from the bioinformatics domain. However, for the sake of analysis, I am trying to pick up certain ...
0
votes
1answer
36 views

Details of DESeq2 modeling a batch effect

When correcting my data for a batch effect using removeBatchEffect, some of the gene expression values become negative. When searching for differentially expressed genes, I do not use the data above, ...
0
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3answers
41 views

What programs account for structural alignment of different parts of distant homologs which have significant structural differences?

If there is a need to perform structural alignment of different parts of distant homologs, which program one should use? Since distant homologs often have significant structural changes, meaning the ...
0
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1answer
36 views

Setting Contrast for DESeq2 results

This question was also asked on BioStars I am trying to recreate this heatmap. How would I compare the four variables: Ly49+/- and MOG/MOGSP to get a single heatmap? Thank you for helping me through ...
1
vote
0answers
22 views

How do I Read a Sam File into a String Using ifstream in C++?

I am trying to read a .sam file into a single string in C++. My end goal is to read this string into a vector, where tabs indicate separations between elements of the vector. After making a vector ...
1
vote
2answers
84 views

Advantages of paired-end sequencing compared to single end

One of the advantages of paired end sequencing over single end is that it doubles the amount of data. Another supposed advantage is that it leads to more accurate reads because if say Read 1 (see ...
1
vote
0answers
11 views

GCF VS GCA or combination of both for pangenomic studies

I have just started to learn bioinformatics and pangenomics. So if this question seems to you pretty basic then I apologize in advance. As we know, NCBI for the genome database, there are two kinds of ...
0
votes
1answer
59 views

TopHat2 versus HISAT2 inner workings

In my intro to bioinformatics course, we mentioned that TopHat2 and HISAT2 will both try to align as many reads as possible to the reference genome (TopHat2 has been superseded by HISAT2). For the ...
1
vote
1answer
17 views

median normalization for proteomics

I am using the data from a proteomics study were the data was log2 transformed and then a median normalization was applied. The data was normalized by groups of conditions (normal, mutant), not for ...
0
votes
1answer
21 views

Pointing Cromwell to local EBS mounted storage on AWS Batch

I'm trying to run the WDL tasks from the GTEx RNA-Seq pipeline with Cromwell using AWS Batch as a backend. I store the STAR alignment index on an Elastic Block Store since my Cromwell server instance ...
0
votes
1answer
45 views

Error using htseq-count: Could not retrieve index file

I have a total RNAseq dataset that I aligned using STAR producing BAM files (sorted by coordinates). I am now trying to get counts for the lncRNA sequences using htseq-count, with the command: ...

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