All Questions

1
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1answer
20 views

Downloading multiple SRA files from several SRA accession IDs does not work

I am trying to download multiple SRA files located in several SRA accessions. Some of my accession numbers are as follows: ...
-1
votes
0answers
20 views

Sequencing Deciduous Plants

Firstly, I'm personally not in the field of Bioinformatics, so apologies if this is a dumb question. Does anyone know of any research that has been carried out on the sequencing of deciduous plant ...
0
votes
0answers
36 views

Is there a read mapper that allows input in SAM format instead of FASTA/FASTQ?

When we get raw sequenced reads in FASTQ format, we usually need to do some pre-processing (QC, demultiplexing, etc.) prior to sequence alignment. The only way to register the results of this ...
1
vote
0answers
9 views

How to paste RSIDs in CADD output

I want to paste RSIDs in CADD output as CADD does not give RSID column in its output. For this purpose I am using bedtools intersect to compare two files and have RSID column in my CADD file. This is ...
1
vote
1answer
27 views

Error compiling HMMER v3.2.1

I tried to compile HMMER v3.2.1 in Cygwin using ./configure followed by make or ...
3
votes
1answer
27 views

Compare two networks of the same genes between two species

I had a set of genes for honey bees. I found the homologues of those genes in the house fly and created a network of the honey bee genes and a network of the homologous fly genes using STRING. I ...
1
vote
5answers
53 views

How to create a .bed file from .fasta?

I have some problems with creating a .bed file for hg19 which I will be able to load on IGV. The fasta file contains rows of this form: ...
2
votes
1answer
29 views

Using Seurat to compare mutant vs.wt

I am interested in using Seurat to compare WT VS. Mutant. I don't know how to use any code or package to test whether when mutant mice, that have deleted gene, got the cluster to combine?
3
votes
1answer
28 views

What is “block-compressed” file in samtools?

SAMtools returned an error message for my gzipped genome FASTA: Indexed block-compressed FASTA file cannot be handled The source code for the message is here. ...
2
votes
2answers
34 views

Can I get the graph generated by cellranger

I’ve run the cellranger analysis pipeline on single cell RNASeq datasets. I can import the matrix and graph-based clusters into R. Doing this I can optimise the dimension reduction and plot cells with ...
3
votes
0answers
21 views

Problem: “Pair-end” reads scRNA seq data (Drop-seq)

In case of Drop-seq, we have paired end data. Read 1: Cell code + UMI (unique molecule identifier) Read 2: The transcript information But I have a problem/doubt with the sample I am working on. ...
3
votes
0answers
50 views

Double-counting coverage of overlapped read pairs

I used samtools depth to calculate the depth of coverage for samples in the whole Exome region using a GRCh37_ref.bed. These samples are sorted and duplicate marked. I ran this calculation on a few ...
1
vote
1answer
28 views

E.coli Sequencing & Analysis

I have been given the task of assembling a 'new' Ecoli genome and analysing the genes present etc. The Ecoli is a new strain, and has been taken and run on a Nextseq 500 in high-output mode with ...
0
votes
0answers
13 views

In Uniprot how do I know which variants are mutations and which are polymorphic?

In Uniprot how do I know which variants are mutations and which are polymorphic? I am looking at P38398 (BRCA1_HUMAN) specifically. Many thanks.
0
votes
1answer
16 views

Continuing analysis based on a log-likelihood ratio? (Comparing methylation between two PoolSeq phenotypes)

I'm trying to get some pointers on where to start on the analysis of my dataset. First, some basic info: Background: We performed Nanopore sequencing of two poolseq samples called UU and DD referring ...
2
votes
0answers
12 views

hgsql not found when running a script despite being accessible on command-line

I am working on macOS. I am following the steps described here to lift over an annotation from the reference genome of C. elegans to another assembly of C. elegans. I have run this code: ...
1
vote
1answer
33 views

ScaleData() from Seurat causes crash on RStudio Cloud

Using the sample data in the 2,700 PBMC clustering tutorial, the session crashes at the ScaleData() step. The progress bar remains at 0% and hangs, followed by an R ...
0
votes
0answers
21 views

scoring matrices computation from transition probability matrix

The transition probability matrix over time t is computed as P(t) = e ^Qt. In order to calculate a general set of transition probability matrices what type of t values can be used ( t = expected ...
2
votes
1answer
31 views

different results coming from biomart online and biomaRt R library

I am playing with biomart in order to get the list of genes associated to a specific gene ontology (GO) term. So, if I use the webservice as in this query: I get at least 50 genes. If I download the ...
0
votes
1answer
49 views

How to get PSSM of protein by protein sequence with python?

I didn't find way that convert protein sequences in FASTA to PSSM by python, and how to write program in python to find PSSM for our data set ? Maybe better to question how to find PSSM from NCBI ...
1
vote
1answer
38 views

Accessing UCSC genome via ssh results in a validation error

I am working on macOS High Sierra. I am following the steps described here to lift an annotation over from one version of a genome to another. I am now just using the example genomes provided in the ...
0
votes
2answers
69 views

Multiple correlation with R

I have a data frame presenting different variables in column and for different species name in rows as follow. In the column a have only one independent variables(Proteome size) and all the others are ...
0
votes
3answers
35 views

How to convert data in gmt format to dataframe?

I downloaded c5: gene ontology gene sets file from http://software.broadinstitute.org/gsea/downloads.jsp I opened the "c5.all.v6.2.symbols.gmt" file in csv format and It looks like below: I want to ...
0
votes
1answer
34 views

Retrieve all genes for a specific gene ontology

I'm having a bit of confusion about how can I retrieve all the genes that are associated to a specific gene ontology. Lets say I need to find all the genes that are associated with this GO entry: ...
3
votes
1answer
41 views

Error correction within the long read

I am going to get some data from plasmid sequencing to identify SNPs on the plasmids. What is done in the lab is the following: The plasmids are purified by size. We amplify the plasmids using the ...
4
votes
2answers
39 views

Group genes by functional categories suming expression values

Using the count of rpkm values from genes in a metagenome sample, I want to group these genes into established categories (for example KEGG or COG). For each sample, my goal is to determine which ...
0
votes
0answers
16 views

Can I calculate maximum parsimony for a binary dataset with morphological characters?

I have a dataset with binary morphological characters. I am wondering if it is possible to calculate the maximum likelihood of a phylogenetic tree for this dataset, but it seems that all of the ...
1
vote
1answer
23 views

What does that mean if there is no bifurcations in my time series single cell data?

I have analysed my time series single cell data with Scuba algorithm but that says that there is no bifurcations in my data and outputted a single chain of 4 states with no branching like below figure:...
1
vote
0answers
15 views

Visual representation of detecting deletion by different read types

I'm having some trouble differentiating between CNV, split reads and read pairs and how each one elucidates the presence of a structural variation, say deletion. Given a reference and donor sequence,...
0
votes
0answers
17 views

From bedtools “genomecov” back to .bed

I have the results of: bedtools genomecov -d... Output: 0 0 10 10 10 20 20 And i want to convert it back to bed file. e....
1
vote
1answer
33 views

Using ONT MinION, why is that we cannot get a full length DNA read?

Here, https://www.youtube.com/watch?v=E9-Rm5AoZGw, ONT claims they can read non-fragmented DNA and that with the hairpin like structure the double strands can be read at once. Then why is that MinION ...
2
votes
0answers
26 views

Why does repeatmasker annotate transposons of length 1?

I am working on Mac OSX. I have downloaded RepeatMasker from www.repeatmasker.org. I have downloaded RepBase from www.girinst.org. I have download the WS266 version of the C. elegans genome from ...
0
votes
1answer
25 views

How do I interpret my phylogenetic tree construction from Glucosidases in the Actinobacteria class?

Dear knowledgeable bioinformaticians, I'm currently pursuing an undergraduate degree and as a result I do not have so much knowledge in this topic. I'm having some troubles understanding my ...
1
vote
3answers
129 views

Replace lowercase characters with -

I have an output from vcfutils.pl vcf2fq with specified minimal depth, and it means that nucleotides with not enough depth are lowercase. I would like to change them to gaps. I could do it in higher ...
0
votes
0answers
26 views

Predicting of predispositions [closed]

Is it possible to predict predispositions of the child, based on only two parental DNA? What algorithms / technologies are used for this?
3
votes
2answers
56 views

Collapse cell barcodes distribution within 1 Hamming distance

I have a barcode distribution from single-cell data, e.g: ...
0
votes
1answer
18 views

Build a Pubmed query given long gene list

I would like to search the literature using the Pubmed search engine for a set of genes that are associated with a brain region of interest. Unfortunately, there are a lot of them. It's possible there ...
0
votes
1answer
16 views

List of human transcription factors

I'm looking for a list of human transcription factor (TF) genes. Where can I find a TF database or how can I retrieve this list from other databases?
3
votes
3answers
53 views

How to convert Bed file to fasta file?

I have Bed file containing start and end of a sequence, and I need to convert it to fasta format, any recommendations?
2
votes
1answer
73 views

Integrative analysis of omics studies using machine learning

I would like to use public omics datasets (ChIP-seq, RNA-seq, and ATAC-seq) from different studies to do an integrative analysis as follow: Normalise samples, within each type of omics, from ...
0
votes
1answer
20 views

Problem with SPAdes installation - no bin folder

I have been trying to download SPAdes for an important project I wanted to do, however, I have encountered a small problem while doing so. It appears that there is no 'bin' folder in my SPAdes ...
8
votes
1answer
174 views

What is the most compact data structure for canonical k-mers with the fastest lookup time?

edit: Results are current as of Nov 7, 2018 12:00 PST. Background K-mers have many uses in bioinformatics, and for this reason it would be useful to know the most RAM-efficient and fastest way to ...
0
votes
1answer
20 views

Mapping RefSeq-ID or NCBI-ID (Entrez-ID) to EC number

I annotated my bacterial genomes using the new NCBI Prokaryotic Genome Annotation Pipeline and now, I want to annotate EC-numbers. In the master annotation file (.gff), I get the RefSeq-ID of every ...
-1
votes
2answers
13 views

levels of factors in the design have non-unique level names after make.names() is applied

When I try to import the data using DESeq2 package: dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Group + Cre) I am ...
4
votes
1answer
23 views

Codon usage analysis for whole genomes

I am new to bioinformatics. So if these questions seem you to a bit childish please forgive me. I have two queries. I am intending to perform a codon usage analysis followed by correspondence ...
3
votes
0answers
34 views

Fastest way to demultiplex bam file based on field

I have a bam file with aligned reads from multiple plates. For each plate I have a portion of the sequence identifier, e.g. HWI-D00310:448:CCG0KANXX:7:1101:2570:1976...
1
vote
0answers
14 views
0
votes
0answers
13 views

Is there a tool that converts fastq to fast5? [duplicate]

We need lots of fast5 files. Anyway i can convert fastq to fast 5 or simulate fast5?
5
votes
0answers
24 views
+50

What is the minimum number of individuals per group required for ADMIXTURE analysis?

What is the minimum number of individuals required per group (population/species) for an ADMIXTURE analysis to be appropriate? Is there a way to determine this number mathematically based on the ...
3
votes
0answers
26 views

Gene not found in Affymetrix expression profiles

I am studying the ABA network in A. thaliana, consisting of HB7, ABI1 and AREB2. The AGI code I was given are, respectively: AT2G46680, AT4G26080 and AT1G45249. I downloaded the following file in ...

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