All Questions

0
votes
0answers
3 views

Pipeline for extracting gene from multiple genomes for use in HyPhy selection analyses?

I have been trying to obtain some preliminary data from HyPhy selection analyses to inform a larger project. I have obtained a number of assembled mammalian genomes from NCBI with the initial goal of ...
0
votes
1answer
5 views

Matching these matrices in R

I have two matrices; I want to convert the row names of first matrix to gene symbol from matched ensemble=gene symbol from second matrix ...
0
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0answers
5 views

What is the purpose of the “fixedSearchFolder” and “fixedCombinedFolder” in MaxQuant?

What is the purpose of changing the fixedSearchFolder and fixedCombinedFolder in MaxQuant proteomics software? Is there any data ...
0
votes
0answers
20 views

Preparing PDB file for modeling with Swiss-Model

I recently starting studying bioinformatics and have a question. I need to build a model of protein using Swiss-Model. First, I need to download a protein record from PDB (for example, 2HZI), then I ...
0
votes
0answers
4 views

How to define TMH boundaries from structures in OPM at the sequence level

I am trying to find which are the transmembrane residues in a given structure. OPM uses PPI to orient TMPs in a membrane space. OPM looks to have the boudnaries at the atomistic level from their ...
1
vote
1answer
29 views

How to interpret UniProt allele patterns?

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the comments POLYMORPHISM there ...
2
votes
1answer
22 views

Is there a safe catch-all adapter sequence for trimming?

I would like to trim/mark adapters using trimmomatic or picard MarkIlluminaAdapters from a series of Illumina Paired-End read fastqs. The fastq files may have been done using different kits or ...
2
votes
1answer
15 views

How to interpret amino acid representation

What is the difference between C383S and C383A? For C383S, does it mean Cysteine(C) position 383 in the sequence and its next amino acid connect to it is Serine(S)?
0
votes
0answers
15 views

How to retrieve the best-scoring Trinity isoform from blastx results

I'm working on a somewhat unusual transcriptome focused on a killer X chromosome. This chromosome has some new genes, with expression levels quite different from their autosomal paralogs. I've found ...
4
votes
1answer
142 views

Splitting fasta file into smaller files based on header pattern

I have to split this fasta files into smaller files and write them into individual files my files ...
0
votes
1answer
15 views

How do I tell featureCounts to ignore fragments that overlap with more than one feature?

I am using featureCounts from the subread package to count the number of fragments per gene in an RNA-seq experiment. I feed it a BAM file with paired-end reads aligned to a reference genome. In the ...
1
vote
1answer
15 views

Retrieving Metabolic networks from WIT Database

How can I get the dataset for all the 43 metabolic networks for this paper: https://www.nature.com/articles/35036627 It looks like the WIT database does not exist anymore.
1
vote
0answers
5 views

I get the following error when using the GSEA software 'Enrichment Map Visualization' tool using the Cytoscape 3.7.1 application

I am trying to visualize a GSEA analysis I conducted using the Broad Institute's GSEA Enrichment Map Visualization, however I get the following error and am not sure what the issue is: any help would ...
6
votes
3answers
47 views

“seed” for various sequence aligners

I would like to know what do we mean by "seed" for various sequence aligners. How is it important? I tried to look online but haven't found a proper definition
1
vote
1answer
59 views

Hits in Primer-BLAST not found with programmatic blastn query

Summary: I'm writing an automated tool for designing Sanger sequencing primers (other tools don't do exactly what I want) that will be incorporated in a production diagnostic laboratory for on-demand ...
2
votes
1answer
30 views

Restriction enzymes with multiple recognition sequences

In a bioinformatics programming course I am currently teaching (using Python, and approached from a mostly CS rather than a biology background) I assigned a project which involves finding sites where ...
1
vote
1answer
25 views

Filter VCF for “CAF=[0.9,0.1]”

Related to this other question but in this case the CAF is defined as "An ordered, comma delimited list of allele frequencies...". I tried using vcffilterjdk and the command suggested by Pierre <...
1
vote
1answer
32 views

Download program for ΔG for TM insertion

I am trying to calculate the ΔG of TM insertion for many protein sequences. Has anyone come across the source code or a programmatic version for the von Heijne ΔG for TM insertion? The web server is ...
0
votes
0answers
15 views

I am getting a parsing error when uploading .chip file to GSEA software

I get the following error when I try to load a .chip file to GSEA software. What is the problem? ...
0
votes
1answer
33 views

What do individual variables mean in PAML?

I'm new to PAML's baseml. I know what ω, κ, π, p represent, but what is the difference between ω0, ω1, ω2 and p0, p1, p2? ref: http://abacus.gene.ucl.ac.uk/software/pamlDOC.pdf
0
votes
1answer
33 views

Finding genes especific to microenvironment

I have RNA-seq .bam files for 3 patients, tumour and its matched derived model, namely organoid, but I don't have any matched normal sample. Differentially expressed genes between a tumour and its ...
2
votes
1answer
86 views

Variant calling without matched normal sample

I have WGS .bam files for 3 patients (tumour and its matched derived model namely organoid) but I don't matched normal sample. If I call variants of each patients (tumour and its matched organoid), ...
1
vote
0answers
39 views

extracting gene names from pubmed abstracts

I have been extracted number of abstracts from pubmed. now I am having a bunch of abstracts of pubmed articles now from this abstracts I need to extract gene names which are included in abstracts.
2
votes
1answer
60 views

Differentially methylated position analysis in a related sample?

I'm trying to figure out how to do a DMP analysis (using minfi dmpFinder) on a related sample (if it's even possible). Right now the code (not written by me) is: ...
4
votes
1answer
43 views

Searching tool to calculate phase/switch error rate

I'm looking for a tool which, given a truth vcf file and a test vcf file, calculates the phase/switch error rate. I performed phasing of a vcf using WhatsHap and want to compare the outcome to some ...
2
votes
1answer
59 views

Running htseq-count over BAM files

I am trying to derive an expression matrix from BAM files using htseq-count on the server. These are bulk RNASeq BAM's by the way. I have read the ...
3
votes
2answers
55 views

Tools for quality trimming at 5 prime?

I'm looking for a tool that is capable to do quality trimming at 5' end and it is configurable. For example, I can choose the quality trheshold, the read length, etc. Any recommendations? I'm ...
0
votes
1answer
37 views

How can I specify an email address in the SLURM snakemake json configuration file?

I am working on a SLURM-based cluster. I am currently using the following slurm json file: ...
1
vote
1answer
21 views

Including Picard tool in galaxy

I am running the Picard tool CollectSequencingArtifactMetrics in galaxy (locally in my pc). The output files are saved into disk and not passed to stdout and (I guess) they can't be passed as output ...
1
vote
1answer
71 views

How to interpret fish plot in R

I am working on subclonal evolution of multiple myeloma. After literature survey, I found people use Fish plot to represent tumor evolution. The example of fish plot can be found here. But I am not ...
3
votes
1answer
40 views

Does UCSC definition for telomere making sense?

UCSC provides a database of telomere regions for each chromosome: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz It reported the telomere section in chr21 as: ...
1
vote
0answers
28 views

Geneland R + Fortran error?

I am helping an undergrad with their project and their thesis advisor has requested they use GENELAND for their analysis. I haven't worked on this sort of analysis, so all I have done is install it in ...
3
votes
1answer
34 views

How can I assign a genomic region into a window using R?

I have asked this question at BioStars but have not gotten any suggestions so far. So, I am asking the community here, perhaps someone here has an idea how I can solve my problem. I am dealing with a ...
0
votes
0answers
56 views

Permanent error with picard

I am sure I set the path right but whatever I am trying the command not working Any help please? ...
2
votes
0answers
21 views

Is there a risk in inference of structural variations using mate-pairs?

Inference of structural variants from short read data is always sneaky (for a question about pair-end reads, see this). Recently I bumped into a paper where they used mate-pairs for inference of ...
1
vote
1answer
24 views

Is there a resource where I can donwload E. coli assemblies grouped by their pathotypes?

I will preface this by saying I'm not a microbiologist, so I apologise for any haziness and I'll be happy to expand. I would like to download the assemblies of different E. coli genomes and group ...
1
vote
1answer
29 views

HISAT2 - are all multi mapped reads reported by default?

While going through the HISAT2 manual, one can see this: Two alignments for the same individual read are "distinct" if they map the same read to different places. Specifically, we say that two ...
0
votes
0answers
11 views

maf file format: Variant_Classification value for non frameshift substitution

I have a vcf containing SNV and MNV (short indells or substitutions), I annotate that file whit annovar and in the resulting txt file I have this row ...
0
votes
0answers
8 views

What is the purpose of 'Folder locations' in MaxQuant?

MaxQuant is a tool for proteomics quantification. In the settings under Global parameters / Folder locations are three folder locations that are possible to be ...
0
votes
1answer
67 views

bedtools unable to open file despite being tab-delimited

I got the following error when attempting to intersect two files. The file below is supposed to be the -a file. ...
2
votes
0answers
18 views

Does the Ziggurat Deconstruction algorithm from GISTIC2 exist elsewhere?

GISTIC2 is a canonical tool in cancer genomics, which introduced an algorithm called "Ziggurat Deconstruction" to deconstruct each segmented copy-number profile into its most likely set of underlying ...
0
votes
1answer
52 views

Assembly by stringtie

I run this cmd ./stringtie G1_sorted.bam -B -o G1.gtf -G Triticum_aestivum.IWGSC.42.gtf -p 4 -C G1.refs.gtf -A G1.abund.tab Error is: ...
3
votes
2answers
70 views

Getting data from fastq by generator

I have a task in a training that I have to read and filter the 'good' reads of big fastq files. I downsampled, got the code working, saving in a python dictionary. But turns out the original files ...
0
votes
1answer
29 views

Error in formation of correlation matrix-(corrupt matrix — dims not not match length)

I am working on a script to create a correlation matrix and mutual_rank matrix from RNAseq gene counts for 57992 genes in 7027 samples. I have already tested this script for a smaller file (for 10,000 ...
2
votes
0answers
59 views

lower mapping rates in salmon v0.13 compared to previous versions

Hi there :) Thanks for the tool! I recently updated to the new salmon (from 0.8... its been a couple years) and I noticed that my mapping percentages change dramatically between the two versions. ...
1
vote
1answer
11 views

cn.MOPS fails with 'missing value where TRUE/FALSE needed'

I am trying to use cn.MOPS to call CNVs on a set of whole exome sequencing data bam files. My script (up to the point where it fails) is: ...
3
votes
1answer
35 views

Error while loading a big file with Cytoscape

I installed Cytoscape 3.7.1 with java 1.8.0_191 in windows server 2012. I have a 7.4 GB csv file (about 1,500,000 reords) and when I tried to load it into the ...
0
votes
1answer
39 views

I need some tips and suggestions for further analysis of NGS expression data (log2cpm)

I am a PhD student who inherited some log2cpm data of expression data from bulk kidney tissue from a UUO(unilateral urethral obstruction) experiment that tests a new drug. The sample material consists ...
2
votes
2answers
34 views

bedtools: get name column of alignment file A

I'm using the coverage function of bedtools to check whether a certain set of regions (file B) has any overlap with known ...
0
votes
1answer
20 views

How to use analysis output in my pipeline

I am running an analysis and I want to edit the output that I received from that analysis. However I cannot define the output name in my pipeline, because after running the analysis it is asking me to ...

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