All Questions
5,471
questions
0
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0
answers
8
views
how to differentiate a DNA fastq and RNA fast q
I have 2 sets of fastq files from another collaborator.1st is Exome and the 2nd one is RNA seq. But both have the RNA in the name but a different ID. How do I differentiate between a fastq file ...
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2
votes
4
answers
142
views
Parallelize or qsub a bash script
I have a bash script that I would like to parellelize to run on multiple nodes. My goal is to run my python sample_script.py script on pairwise comparisons of samples to see if their variants are a ...
- 21
1
vote
0
answers
22
views
Title: Error merging VCF files: "The REF prefixes differ: G vs A"
I'm trying to merge two VCF files, but I'm running into an error message that says ...
- 11
2
votes
1
answer
32
views
Dealing With Manta Limitations
I am trying to figure out a way to remove the limiting factors that Manta says it cannot handle. To quote from the Manta page:
The following limitations exist on the input BAM or CRAM files provided ...
- 43
2
votes
2
answers
24
views
RNAseq alignment: best practices for aligning to multiple isoforms?
I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed genes between experimental conditions.
Many of my (de novo assembled and ...
- 23
0
votes
4
answers
52
views
Can you infer orientation from vcf file data?
I have a dante labs dataset that I would like to cross reference with SNPedia but I am unclear about orientation. I've read the info on SNPedia and other places about it but I just don't get it yet. I ...
- 131
0
votes
0
answers
18
views
How to check average gene expression for each of 2 conditions within a cluster in scanpy?
I used scanpy to do DE analysis for 2 conditions within a cluster.
I set it up like shown here:
...
- 103
1
vote
1
answer
40
views
Analysing the Effect of a Drug on the Morphological Changes of a Cell Type
We came across a project in our lab that no one exactly knows how to approach. Since, I know a little bit of Python programming, this project was assigned to me.
There is a data from a randomised ...
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3
votes
1
answer
40
views
Passing strings for password, email authentication and download link
Hi I am downloading the data from a website which requires authentication of email_id and password before the download. They then provide the download link which is used to download dataset. This ...
- 351
2
votes
1
answer
77
views
Manta "--exome: command not found"
I am using Manta (https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md) but whenever I try to specify the --exome command using the following code ...
- 43
2
votes
1
answer
22
views
Using ticks on the x axis or a scale bar when visualisizing a phylogram?
When visuliazing a phylogram is it preferable to show ticks on the x axis or a scale bar?
Given an example tree with branch lengths in newick format ...
- 43
4
votes
1
answer
34
views
What is the NCBI's definition of an "atypical genome"?
Using the new NCBI Datasets platform, you can browse the collection of genomes associated with one or more taxa. For example, searching Pseudomonas aeruginosa returns 19,878 genomes as of 29 March ...
- 553
-1
votes
1
answer
52
views
Variants list to aminoacids
I have the sequencing data of a Monkeypox virus sample. I have the list of variants extracted from Nextclade and I want to find the corresponding aminoacids substitution.
For example I have the ...
0
votes
1
answer
47
views
Help with analyzing SNP data for three patient groups
I am currently working on a project where I have genetic data for patients classified into three different groups. Specifically, I have information on 26 SNPs for each patient. I have recorded each ...
1
vote
0
answers
22
views
ucsc-bedgraphtobigwig throwing memory allocation error
I installed the latest ucsc-bedgraphtobigwig (v377) with conda in a new enviroment enviroment inmy WSL2.
conda install -c bioconda ucsc-bedgraphtobigwig
However, ...
- 11
1
vote
1
answer
32
views
Running cellranger on scRNASeq data with feature barcoding (10x + antibody capture)
I can't seem to find a clear answer to this question, so here it goes:
I have sequenced scRNASeq + scVDJSeq (TCR) data, which has been sequenced using feature barcoding from 10x genomics, via antibody ...
- 836
-2
votes
1
answer
57
views
Histogram plot using R/python with two variables[BC and Control] and their corresponding gene names
How do we plot histogram in R\Python with two variables[BC and Control] and their corresponding gene names examples is below:
Thank you,
2
votes
2
answers
138
views
0
votes
0
answers
24
views
SKAT method in R
I have data that looks like this: 3 column SNPs their gene based on Annovar and a p-value for every SNP. What I would like is to aggregate the p values for every gene.
...
- 29
0
votes
0
answers
36
views
How would you define a set of active genes from a bulk RNA-seq experiment in one biological sample? [duplicate]
I am trying to identify genes that are overall considered to be "actively transcribed" in my cell line of interest for some downstream analysis.
What would the approach be for defining this ...
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3
votes
1
answer
64
views
Extract specific nucleotide base position for query and subject from text file
I have an input file looks like this:
...
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2
votes
1
answer
29
views
Nextflow Error: failed to read header from "-"
I am trying to run my nextflow pipeline, and have gotten this error:
samtools sort: failed to read header from "-"
I'm not sure why this error is ...
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3
votes
1
answer
32
views
Download all pubmed central article ids that have a keyword appearing in their titles/abstracts and also falling between two dates
I am using the following code to download all pubmed central article ids that have a keyword appearing in their titles/abstracts and also falling between two dates. The code seems to work when I ...
- 175
0
votes
1
answer
24
views
Any existing workflow on Terra that can run multinomial logistic regression?
I need to run multinomial logistic regression on a smaller set of variants e.g. using Trinculo. May I know if there's any existing workflow on Terra that can do this? Thanks.
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2
votes
1
answer
35
views
Improving conversion of abricate tsv file to gff3 file
Since such a neat solution (abricate tsv to gff3) was provided by Steve, here are few other steps that I am looking to add so that the script progress to logical maturity to be usable by many others.
...
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1
vote
1
answer
46
views
RNAseq: Why would using a more complete scaffold reduce DEGs?
I have a set of RNAseq data for a couple of relatively under-studied species.
They're fungi, of the order Hypocreales. The assemblies we're working with are de novo - reference seqs don't actually ...
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1
vote
0
answers
14
views
Generating gene signature for sample classification and survival analysis patient cohort
This is from this paper
The LSC17 score is calculated for each patient as a linear combination of GE of these 17 genes weighted by regression coefficients that were estimated from the training data as ...
- 111
0
votes
1
answer
37
views
complete the res type in sdf
I use the diffdock (link to diffdock on github) to dock a peptide with protein and this tool give me a ligand in sdf file format. I traslate this ligand sdf format file to a pdb format file and find ...
2
votes
1
answer
36
views
Why are asymmetric distributions an issue for GSEA?
I'm reading Subramanian et. al's (2005) original GSEA paper. In the paper, the authors mention the following:
We noticed that the use of
weighted steps could cause the distribution of observed ES ...
0
votes
0
answers
15
views
Does GSEA assume that genes sets must involve genes that are POSITIVELY correlated with each other?
I'm reading Subramanian et. al's (2005) original GSEA paper. Because GSEA increases the running sum statistic the most when genes appear close to each other (and hence yields a large ES score), it ...
0
votes
0
answers
9
views
Molecular dynamic simulation, reconstuction of protonation pattern of a protein from PDB file without resolvent hydrogen
I'm trying to build a topology of a protein using GROMACS. The pdb file do not include coordinates of hydrogen atoms. So I was wondering how to assign appropriate protonation states for each residue. ...
-1
votes
0
answers
32
views
How can I process fastqs generated using the inDrops protocol into a counts matrix?
Cross-posted on Biostars
I'm trying to re-analyse scRNA-seq data from a recently published manuscript. The methods state that the data was generated using the inDrops protocol, but doesn't mention ...
1
vote
1
answer
33
views
Convert Abricate output tsv file to gff3 format
I have a tsv file generated from abricate (https://github.com/tseemann/abricate). I need to convert them to gff3 format with certain columns retained, certain columns reordered, while other columns ...
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2
votes
0
answers
30
views
Simes method in R
I have data that looks like this: 3 column SNPs their gene based on Annovar and a p-value for every SNP. What I would like is to aggregate the p values for every gene.
...
- 29
3
votes
1
answer
40
views
Nextflow Pipeline: Unexpected Input "{"
I'm attempting to run a nextflow pipeline and have begun getting unexpected output for a few of the processes in my pipeline. I believe this to be a syntax error, but I am not sure where to correct it....
- 55
2
votes
1
answer
33
views
sra toolkit fastq-dump comand not terminating
I ran the following command trying to download a fasta file from NIH but the command doesn't seem to terminate and I get no output file in my repository:
...
2
votes
0
answers
30
views
Extracting positions from PAF files in order to extract sequences from a Fastq file with Python
I have used Minimap2 to create a paf file by aligning a Fastq file against itself. Now from this Paf file I can see where the reads overlap, and I want to take these positions, and use them to extract ...
2
votes
0
answers
44
views
STACKS: process_radtags only reads 1 input file and returns >90% barcode not found drops
I am trying to demultiplex some paired-end ddradseq data and am running into an issue with STACKS in that the program only seems to read 1 of my files for input (there are 2) and also results in over ...
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2
votes
0
answers
56
views
Cut and Tag analysis
I am trying to do Cut and Tag analysis for a set of files and I want to perform a procedure called Tn5 normalization of samples.
The basic goal is to generate bedgraph files and does normalization ...
- 143
2
votes
0
answers
24
views
PROKKA setupdb / cmpress error
I am trying to run --setupdb in Prokka, but I'm getting this error that I can't seem to find the answer for.
When I run
prokka --setupdb
I get
...
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1
vote
1
answer
32
views
Given a FASTA file with a set of genes, how do I determine that set's conservation among a genetic order?
Given a set of genes in a FASTA-formatted file, for example: exFasta.fa, what is the best way to determine how well conserved the genes in that file are among an ...
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0
votes
0
answers
23
views
Calculating total number of Unique gene in every genome from ROARY pangenome output
I performed a ROARY from 100 genome. I got several file including gene_presence_absence.csv from the results. I want to know how many unique gene(unshared gene, based on blast homology, same gene (...
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1
vote
1
answer
15
views
file order after nextflow groupTuple
Below is the code from nextflow site (https://www.nextflow.io/docs/edge/operator.html#grouptuple).
For the output, the first is A B C, and the second is C, A.
Is there a way to make the output like ...
- 45
0
votes
1
answer
53
views
Is my reference sequence too small?
I'm trying to map ONT long reads to a portion of a gene I'm looking at. The region is about 25bp long. When I search for the region in the document it pulls up the sequence in every read but when I ...
- 453
1
vote
1
answer
45
views
To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?
I love that Deseq2 has altHypothesis="lessAbs" !!!!!!! I've used it a ton for RNA-seq. However, now I'm working with mass spect data using limma. Is there a way to make limma do the same ...
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1
vote
0
answers
25
views
From SMILE get Amber force in Python
I have a list of SMILES of small molecules and I want to be able to simulate these molecules with an Amber force field in Python. Currently, I use RDkit to convert the smile into a PDB file:
...
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2
votes
2
answers
92
views
How to generate rsid values locally from VCF file
I recently used Dante to obtain a WGS and have downloaded several files produced during this process. There is a file that ends '.vcf' which I did think was a VCF file but I'm not sure now after a ...
- 131
1
vote
0
answers
13
views
How can I programmatically retrieve all alternative gene names from Wormbase?
I'm trying to get all C. elegans genes from Wormbase programmatically, as well as all of their alternative gene names. To do this, I'm using intermine.
I was able to obtain all genes, but not ALL ...
1
vote
0
answers
23
views
Project Plink eigenvector from one group on top of another group
I have 1 bcf file called with individuals from two groups, one which is my samples, another which is a reference panel.
However due to my samples having a limited amount data, when i simply run Plink ...
- 85
0
votes
1
answer
48
views
Replace a string in a column of a text file based on matching string listed in another file using linux
I have multiple sets of files, so I grepped the list from a column in a seperate file such as file1.txt. I want to change all other files by using this file1.txt based on a matching string.
for ...
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