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3 views

Asking for Docking programme

I'm tring to do my M.Sc. research and i Have to do Docking to save some money as I cant try all the compound that I'm working on. what is the best Protein-Ligend Docking programme? And anyone has ...
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0answers
13 views

Nanopore FASTQ header specifications

Is there a specification anywhere for how a Nanopore FASTQ header should be formatted?
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1answer
17 views

How I deal with this expression set?

I have a gene expression raw counts like below for 16 patients ...
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1answer
22 views

WGCNA module preservation analysis

I have case control studies,4 different condition where I have 1 control and against which I'm have 3 comparisons to make. I did WGCNA for individuals samples .Here I have the kept the number of ...
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0answers
17 views

fixing chromosome with new contig

I want to fix a chromosome of around 50-100Mb (chr.fasta) for a region that is missing a few kilobases of data. I have the missing sequences together with a window ...
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0answers
23 views

Blood analysis devices: how and where is the data saved

I've read that there are blood analysis devices that can automatically determine the data for each specified analyse. You can expect to get the results in less than a day. Q: How and where do they ...
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0answers
16 views

How to segment genome into homozygote/heterozygote blocks based on RNA-Seq data

Given a RNA-Seq data of a progeny between two inbred lines (for example an F4 plant which was derived from two inbred lines (parents) and the F1 selfed 3 times; however this is probably not crucial ...
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1answer
22 views

Tree cut issue in WGCNA

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0answers
15 views

Is there a way to extract reads assigned to a particular taxonomic node from SRA data?

I've noticed that SRR submissions have an 'Analysis' section, where one can see what organisms are enriched in the sample; there is even a great graphic display that uses Krona to highlight what ...
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1answer
38 views

correlation between transposon and gene

I have two matrix identical in N° of rows and columns. In the first matrix rows indicate transposable elements and columns indicate samples. the matrix show the degree of expression of each element ...
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1answer
49 views

Filtering fasta files by ID

I have this code to filter some IDs from a fasta file: ...
1
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1answer
22 views

What do the symbols mean in minimap2's gap cost equation?

Heng Li's paper on minimap2 is understandable to me right up until the moment that it gives this definition of gap cost: 2.2.1 Alignment with 2-piece affine gap cost Minimap2 performs DP-based ...
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2answers
39 views

Is there any way to align ChIP-seq reads to telomeres?

I know that telomeres are highly repeated sequences, but is there any way to retain any reads that map to these regions (on HG38)? I recently managed to find some protein binding to centromeres, ...
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2answers
52 views

read and matching pattern with python

I have read the content of a text file into pandas and needed some help matching the pattern. Here is the pattern, where a can any number greater than zero and <...
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2answers
35 views

Which correlation method to compute the correlation score between different clusters of Sc-RNAseq data?

I'm analyzing single cell rna-seq data and trying to compute the correlation score between different clusters. Wondering how to choose the correlation method("pearson" (default), "kendall", or "...
2
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1answer
24 views

Confidence Interval with Wilcoxon Test in Python for log-normal Distribution

I have a couple arrays of dN/dS scores, and I would like to calculate the confidence interval for each array of data. dN/dS scores are not normally distributed but are log-normally distrbuted, so I ...
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2answers
36 views

Smith-Waterman Pairwise Local Alignment Algorithm

I have written a R code for Smith-Waterman (SW) algorithm. I wanted to check the results of my code with online examples. In all cases -except one- I found the same alignment. So there is this one ...
1
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0answers
22 views

Human Cell Atlas - cell annotations

Human Cell Atlas Preview Datasets have been available for a while now (there was some discussion about that earlier). However, although the raw data is available, cell labels are not (for example, ...
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1answer
87 views

Doing plot with this data

I have normalized expression values of some genes in some patients and the how many days they have survived from their diagnosis with cancer like below EDITED I have taken mean of the expression ...
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1answer
48 views

How many types of DNA methylation are there?

My current understanding is: bases A or C can become methylated due to interaction with a methyltransferase these methylations ...
2
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2answers
56 views

How I swap rownames in these data?

I have a microarray gene expression matrix like this by weird gene IDs in rows. > head(mat[1:10,1:5]) > dim(mat) [1] 39302 76 > There is matched ...
2
votes
1answer
14 views

RPGC normalisation creates artefacts at centromere

I am studying ChIP-Seq data in HeLa cells and I've started using the RPGC normalisation of deepTool's bamCoverage. MACS2 also uses this normalisation for its peak calling. I am seeing a large number ...
1
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1answer
31 views

storing SNPs in the genotype file for each chromosome in a separate file

I have already asked this question in another forum but have not got an appropriate answer, so wondering if anyone here can help me? I have a big file with over 3 million columns (SNPs genotypes) and ...
1
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1answer
26 views

Extract reads from bam files by their @RG

How could I extract reads from bam files by their read groups @RG ?, I've got one file containing all reads for 5 samples, the SM is appears NONE, So, I want to extract each sample reads by the @RG ...
1
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2answers
28 views

How to retrieve values from one table that corresponds to the values in another table in R

I have following table. structure(list(n = c(29L, 11L, 10L, 10L), domain = c(1L, 5L, 6L, 32L)), row.names = c(NA, -4L), class = c("tbl_df", "tbl", "data.frame")) ...
1
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0answers
11 views

What's the point in estimating the background distribution in probabilstic models of motif finding such as MEME (mixture model with EM) or some HMM?

I suppose that in the database searching for homologous sequence using the profiles created by whether MEME (represented by a PWM) or a HMM (represented by some profile HMM) make use of the log odds ...
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2answers
23 views

R WGCNA error code

I am using WGCNA to identify Consensus modules. I get a warning message when completing the following step: Call the network topology analysis function for each set in turn Warning: ...
1
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1answer
18 views

Convert or extract Seurat object as the input of FateID

I am currently using Seurat to do the scRNA-seq clustering analysis. After this, I am planning to use FateID to do the downstream analysis, could someone teach me how to convert or extract a Seurat ...
2
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0answers
41 views

Convert PAF format to SAM/BAM format

I have a bunch of PAF files resulting from the alignments of fastq files on a reference genome with minimap2. I would like to convert them into SAM/BAM format so I can use ...
1
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1answer
33 views

where to find pathogenicity metadata for E.coli genomes

I have a list of about 900 E.coli genome ids (Genbank plus NCTC ids), e.g.: ...
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1answer
44 views

awk find pattern

I am trying to find this pattern on a large file but the output doesn't look good. The output doesn't seem to reflect the pattern. ...
2
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0answers
18 views

How to load output from the kegg API in biopython into a pandas dataframe?

Biopython provides a (bit unintuitive) API to access KEGG. I am trying to make use of it, but the output is quite unhandy as a string. What is the best way to parse the data into a ...
1
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1answer
41 views

Is it okay to use deeptools bamCompare (SES normalization) for comparisons across different ATAC-Seq datasets?

We are trying to use deeptools for analysis of ATAC Seq datasets. We have datasets with different sequencing depths and are wondering if bamCompare's SES based normalization is appropriate for ...
1
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2answers
100 views

too long header for fasta file

I have a fasta file, like this: ...
1
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0answers
25 views

vcf tools Error: Require Genotypes in VCF file in order to output Fst statistics

I want to calculate Fst by vcf tools and GATK. I did this steps: for creating gvcf: gatk HaplotypeCaller -R ref.scf.fasta -I input.bam -ERC GVCF -O out.g.vcf ...
1
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2answers
67 views

How to define an outgroup to build a robust amino acid tree

I am trying to build a robust amino acid phylogeny with adequate robustness support (see previous post: How to make a robust amino acid phylogeny with adequate robustness support). This is a brief ...
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0answers
45 views

Selecting genes with more contribution from PCA

I have RNA-seq data in response to treatment vs non response; By machine learning I selected three principle components likely can predict the response based on the gene expression. Now I have ...
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3answers
60 views

match two files and check if position of chrom is within exon region

I have two files, file1 and file2. I want to match file1 chrom with ...
1
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0answers
38 views

How to troubleshoot access to tabix file via http or https?

I have some BED files that I have compressed with bgzip and indexed with tabix. I am using version ...
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4answers
62 views

Merging two files together

Is it possible to merge two files together using awk? I have two files with matched Chrom and pos column file1 has the columns ...
0
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1answer
70 views

How to edit the headers of multiple fasta files from multiple folders? (recursively)

This is an expansion of my previous question, How to edit the headers of multiple fasta files from multiple folders? My directories are organized as follows: one main directory, in which I have ...
2
votes
2answers
42 views

What value of reference RMSD after docking simulation from any starting coordinate would be considered outrageous to have?

I need to lightly verify a set of docking simulations from the reference RMSD of the outputs, and as we all know reference RMSD depends on the initial coordinates of the ligand set. What value of ...
0
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1answer
46 views

Investigate the effect of street-light regime on insects

I need advice on a suitable analysis of a dataset that has an awkward design - because we investigate a real-world situation -we have two sites (A,B) where we can conduct the research. The hypothesis ...
1
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1answer
74 views

Sequencing center returns data in several files

We send some samples to sequence and we got several (fastq.gz) files for each sample. The files are distributed at two or three folders with different dates (more than a week apart). The dates of the ...
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1answer
41 views

Filter out other character after the genotype

Is it possible to filter out all the characters that come after the genotype, for example, I have a data ...
1
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1answer
38 views

awk find Sickle cell anemia from father, mother, son, daughter

I have a file where i what to check for a pattern below and print out all the lines that matches the pattern but the output is empty. here is the pattern that i am looking for. Father = 1/0 or 0/1 ...
1
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1answer
39 views

Weird phylogenetic tree

I am new to research. As part of my MRes, I am required to create a phylogenetic tree(s) of my genes of interest. I am currently blasting (tblastn) my genes of interest from S. mediterranea against ...
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3answers
45 views

How to convert a list of genes to one element per row?

I got two lists of about 300 genes from my GO analysis, like the following: ...
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0answers
38 views

How to obtain the extended unaligned bases of the read in reference based genome assembly?

I did illumina read mapping based on a particular gene sequence (reference sequence) using the following command, ...
0
votes
0answers
15 views

Help understanding why a particular pair in a set does not form a breakpoint for the Breakpoint Reversal Sort algorithm

S = { 8, 2, 7, 6, 5, 1, 4, 3 } The sort will be performed on the set including 0 and n+1 to give S' = { 0, 8, 2, 7, 6, 5, 1, 4, 3, 9 } My textbook lists the breakpoint subsets as follows: ...

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