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0answers
6 views

Protein ligand docking: how to convert <protein>.pdb to <protein>.maps.fld?

Hello I'm helping to develop a cloud docking tool for screening compounds, similar to Swissdock but with mass throughput and GPU optimizations. Specifically helping screen existing drugs against ...
2
votes
1answer
11 views

STAR quantMode vs RSEM vs Kallisto

I recently discovered this Snakemake pipeline for RNASeq that uses STAR's quantMode to quantify gene expression for DESeq2 differential expression analysis. In the past I've always seen the workflow ...
1
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0answers
6 views

What's the difference between Procheck and Whatcheck?

I'm currently using Procheck to check a protein backbone. The process is: Determine backbone phi, psi, and omega angles Compare to known angle distributions to identify outliers, and angles in ...
0
votes
1answer
14 views

How to filter a SAM file by a bed file?

I have a large BAM file and I want to filter it by just what's defined in a bed file, and write it to a new file. Is it possible to do this with samtools, and if so, how? Is there a better tool I ...
0
votes
1answer
8 views

Can I get longer contigs by changing MEGAHIT settings?

My current settings are megahit -r input.fq --num-cpu-threads 32 --min-contig-len 300 --presets meta-large -o output. I picked the 'presets meta-large' because I am ...
0
votes
1answer
39 views

How I change a function not to need an input

There is a function does need an input as selected genomic site across genomic regions. But my genomic region bed file already is a subset of interesting site (like promoters). I want this function to ...
3
votes
2answers
21 views

Is there a “definitive” database for Mobile Genetic Elements?

This isn't quite my speciality, but I've been tasked with finding any evidence of Mobile Genetic Elements (like transposable elements, retrotransposons, bacteriophages, etc.) within some WGS samples. ...
2
votes
1answer
25 views

Snakemake: Migrating from deprecated cluster.json to new profiles.yaml

I am an avid user of Snakemake. Recently we have been refreshing our pipelines and I saw that a cluster.json file is no longer the recommended way to store the cluster configuration. I used to start ...
1
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0answers
15 views

SwissProt Proteins into my Jbrowser

How is it possible to get the SwissProt Proteins into my Jbrowser in the same way like shown below? Thank you in advance,
1
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0answers
22 views

bwt suffix array construction

I found a very good link to generate bwt suffix array in BW based tools. @user172818 provides a nice code. could anyone tell me how to store SA elements' original position in the original string?
1
vote
1answer
29 views

How can i get data set of illness and not illness people?

I'm new to bioinformatic .. i'm reading a paper and what i got that they made a classification for the people if they have a sequence of a disease or not ... ...
1
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2answers
36 views

How to create a .phy file for constructing a phylogenetic tree?

I'm new here. I need to construct a phylogenetic tree from 16s Sequence data (merged 151 bp) and color the branches/nodes based on my experimental conditions. From this blog, it looks like I need a ....
0
votes
0answers
19 views

What are the meanings of these transcript ids?

I have three types of transcripts for Rosa chinensis "Old Blush" homozygous genome v2.0 from GDR genome browser. ...
-4
votes
0answers
47 views

How I remove variants ovelapping common genomic ranges? [closed]

I have a copy number file like ...
-2
votes
1answer
35 views

How to generate ultrametric phylogenetic trees?

I have generated rooted species tree with 1000 bootstraps by RAxML. Further, I need to generate ultrametric tree for the same. Therefore, Please suggest me how to generate ultrametric tree from the ...
2
votes
2answers
51 views

Get start and end coordinates per chromosome

I will use GATK for SNP calling (HaplotypeCaller). I need to feed the interval file in the command, otherwise I get errors (even though I want to use the whole genome, not a subset - btw it's not the ...
1
vote
0answers
42 views

Scientific names of taxids with kraken 2.0.8 beta, command kraken2 --use-names error

I am running kraken 2.0.8 beta to do taxonomic classification of micorbiota data coming from a MinION run based on the 16S gene. To do so I am using the pre-bult kraken SILVA database. I managed to ...
1
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2answers
23 views

select unique names while removing the duplicates from a column

I have a file with Ensembl gene and Transcript IDs : I want to retain only the first entires from both the column so that the output looks like this: ...
2
votes
1answer
30 views

RepeatMasker annotation

I collected my own denovo library using many different tools Pipeline (structure-based ) and I updated all the headers corresponding to RepeatMasker format, to obtain Repeat coverage in the genome and ...
1
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0answers
28 views

Permanent error with maftools

I want to remove variant including in copy number changed area by maftools but I am permanently get this error ...
2
votes
1answer
31 views

Using cellranger for non-10x data

I'm trying to use cellranger to mkfastq and then count and aggregate single-cell data. This ...
1
vote
1answer
84 views

How to initiate RNA-Seq analysis of TCGA files?

I want to compare RNA-Seq datasets obtained from the TCGA to investigate how my gene of interest is implicated in different types of cancer. I'm trying to download the data from the GDC Data Portal (...
1
vote
1answer
30 views

How to calculate Centimorgan lengths from run lengths in one-to-one dna profile comparison

For easier management of a database of dna profiles, I'm creating a tool to perform one-to-one matching on two profiles with snp genotype information. Basically, something that works similar to ...
0
votes
0answers
26 views

Simulating RNA Editing

I'm pretty new to bioinformatics and I have been looking for a way to simulate rna sequencing with editing, specifically A to G, but didn't find anything i could use. I tried using flux simulator but ...
0
votes
2answers
35 views

Q: What analyses can I perform with a completely phased genome assembly?

Phasing a genome is the process of determining which variants lie on which copy of each chromosome. For example, position 5,430,500 might have an A on the paternal chromosome, but a T base on the ...
0
votes
1answer
17 views

Why my bim file doesn't match to my ped file as the Plink documentation suggests?

Plink documentation about .bim says the columns 5 and 6 are the Allele 1 and Allele 2 respectively. The documentation about the .ped in turn, says "...The first six fields are the same as those in a ....
1
vote
0answers
14 views

How can I find genes of fundamental metabolic processes for an organism?

I want to find genes of fundamental metabolic processes in the Phytophthora cinnamomi genome. I'm using the genome sequence deposited in the NCBI and I'm searching ORF by ORF, using the ORF finder (...
1
vote
0answers
48 views

How to get the GO information for all the human genes?

I would like to find a list of all the human genes and their proteins’ functional classification. The Gene type attribute on ensembl.org is not specific enough, ...
0
votes
0answers
21 views

Why the gene symbol aliases have significantly different sequences?

"Aliases" or "Synonyms" should represent the same gene but with different names. But when I try to find the sequence of one alias and try to match with another alias they are significantly different. ...
1
vote
1answer
68 views

Detecting whether genome is genetically engineered?

Is there a methodology for detecting whether a genome has been tampered with by a biologist? For instance, say there has been an ebola outbreak such as in "The Andromeda Strain". Is there a way a ...
0
votes
0answers
15 views

homer differential accessibility analysis

I ran homer differential accessibility analysis using this command getDifferentialPeaksReplicates.pl with 7 replicates of Granulocyte monocyte progenitor(GMP) vs Monocyte(Mono) Im bit confused when I ...
0
votes
0answers
21 views

How can I open the 16S_silva.installation.sh in kraken2?

I installed kraken2, which includes the 16S silva database. Indeed I see 16S_silva_installation.sh. How ca I install it?
2
votes
1answer
27 views

Why do these NCBI representative genomes for ape species have no Y chromosome?

I recently downloaded a genome from NCBI for chimpanzee and was surprised to see no Y chromosome. I added in one from a separate accession and carried on, but then today went to do the same for ...
-2
votes
0answers
19 views

Marked sequence search on genomes [closed]

Where does one gets fullest influenza database and 2019nCov? How does it looks like? It's just a string? I have an idea, I want to correlate virus with existing viruses that have vaccines. I could ...
1
vote
1answer
45 views

Index a BAM file using pysam

(How) can you index a BAM file using pysam? When I tried the intuitive pysam.index I got: ...
1
vote
1answer
33 views

How to visualize called narrowPeak files in UCSC Genome browser or IGV?

I have called peaks using MACS2. Then I got a narrowPeak file like this. ...
0
votes
2answers
32 views

Variant calling for a subset of genes using whole gneome sequencing data

I have few 100 raw fastq files from whole-genome sequencing data and I would like to map these files to a set of genes only (and not whole genome) so as to find SNP's associated with them. Can anyone ...
1
vote
1answer
17 views

Running tophat dockerfile in background

I need to use tophat2 to align some sequences, and I wish to use the docker container. These are large sequences so it will take a long time, plus I'm working on a university server so the chances of ...
1
vote
3answers
74 views

Edit all the fasta headers using awk

kindly your comment highly appreciated have more than 4k header sequences look like: ...
1
vote
0answers
53 views

Finding common and unique data set by comparing two files based on their column and to split the columns multiple strings to print in output

I have very large sizes tab-delimited .vcf files and want to match these two / or 3 files based on their position and print to a new .csv file File structures: File_1: tab-delimited file (.vcf) ...
0
votes
1answer
58 views

Vegetable databases usage

Good morning, I'm aligning with blast some species, against all nt database to analyse the vegetables. However, in some cases we have species of animals mixed with vegetables and want only to detect ...
2
votes
3answers
32 views

How to find a homolog that has a PDB structure available

I tried to find a homolog that has a PDB structure available so I can use this PDB file for comparative modeling. I ran a BLAST search but none of the search results seemed to have a known structure. ...
1
vote
0answers
30 views

Algorithmic Information Measurement of Human Genome Databases?

What is the highest data compression ratio achieved on a population of genomes measured to include the compressing algorithm itself? The size of the compressed database approximates its algorithmic ...
-3
votes
0answers
57 views

Converting this data frame to a heatmap

I have CPM values for response to a drug in two RNA-seq set up. I have grouped the patients to responders and non responders to this drug and I have done pathway analysis. This is my data ...
1
vote
1answer
37 views

Question: How to simulate 100k samples having 40 million SNPs in a proportion of case:control=30:70?

Note: this question can also be found on Biostars I need to perform a stress test in a GWAS tool and the duty demands a dataset (plink format) having 100 thousand samples, having 40 million SNPs in a ...
0
votes
1answer
20 views

VCF's unknown ('.') values causing problems for GATK's Liftover Vcf

I am having a tough time calling LiftoverVcf in GATK. I have concatenated all of the Vcfs of interest and removed rows with problematic values but now when I run LiftoverVCF I get the following error: ...
0
votes
1answer
35 views

Griding ggplot object in r

I have this data frame head(d) ...
0
votes
1answer
12 views

how to get FlyBase ID conversion table

FlyBase uses systematic naming of genes, transcripts and proteins in a format FBtypeNUMBER. However, the numbers are not the same for genes and their products. For ...
4
votes
1answer
53 views

Can I submit a R package to Bioconductor or CRAN if I have already published it a journal?

I have written a bioinformatics package in R that I want to publish in a bioinformatics Journal. Presently, I am maintaining a local repo of that package and I want to put in the Bioconductor ...
0
votes
0answers
9 views

Pfam search using hmmer but only for a specific taxonomy

I am trying to do a de novo assembly using Trinity. Using Transdecoder and blastp/hmmscan search to do annotation (using Uniprot/pfam databases). https://github.com/TransDecoder/TransDecoder/wiki . ...

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