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12,241 results • Page 1 of 245

I have a large fasta file of new species (scaffold assemblage), I want to find extract a particular protein sequence. I also know a protein...I have a large fasta file of new species (scaffold assemblage), I want to find extract a particular protein sequence. I also know a protein sequence

fasta alignment blast

updated 4 hours ago • anna

Hi, can i ask you if there is a genbank file format in which the information of the row /product is merged with the row /locus tag? The reason is that in CLC it's useful to have the information about the gene product in the first

gbkformat

updated 6 hours ago • alenew.am

research paper. I have seen many pdbs have less residues in a chain of a protein than the full FASTA sequence. Most likely, the cause is that they were unmodeled due to its going missing during the crystallization phase...1ZM1][2]. Here in chain B, the last couple of residues were unmodeled. Should I use the shortened FASTA from pdb or should I use the full FASTA for my dataset? [1…

PDB FASTA

updated 14 hours ago • Nafi

and one set of reverse reads (by simply concatenating the respective files)* and then use these merged datasets for mapping with BWA-MEM2? Or do I need to analyze each lane independently and then merge the output data somewhere

GenomeAssembly BWA-MEM2 Hi-C

updated 17 hours ago • Winter

about the genomic gVCF file. I wonder that since gVCF contains the non-var block records, why after merge all gVCF, there are still some NA in the merged gVCF file? And in general, how many loci can be sequenced for each sample in

WES GATK VCF gVCF

updated 3 days ago • zihanss

Hello! I have a multiFASTA file that contains a set of aminoacidic sequences that I want to compare in terms of sequence identity, what tool do you recommend me for this? I want all vs all comparisons so I can build a heat map.

protein FASTA alignment

updated 5 days ago • v.berriosfarias

MuSE Variant Aggregation and Masking" workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking" ) GDCdownload(query) maf <- GDCprepare(query) ``` The issue came out when this statement runs: `maf <- GDCprepare

TCGA GDCprepare

updated 5 days ago • glaciya2018

I have some annotated genomes both with prokka and pgap. Pgap will output gff files with fasta sequence at the end (annot_with_genomic_fasta.gff). I tried running roary (3.12.0) on the pgap annotated *_fasta.gff...tRNA;inference=COORDINATES: profile:tRNAscan-SE:2.0.12;locus_tag=pgaptmp_004502;product=tRNA-Glu ### FASTA >lcl|GCA_007218495.1 Salmonella enterica chromosome, whole genome sho…

pangenome PGAP NCBI roary Prokka

updated 5 days ago • pramach1

I have 2 samples, each a different condition). I will refer to them as sample1 and sample2. What I did is I created a Seurat object for each one and then merged those 2 Seurat objects together... I just started with scRNA-seq analysis and not sure if this is the correct way to go about...I have 2 samples, each a different condition). I will refer to them as sample1 and sample2. What I did i…

clustering subclustering scRNAseq

updated 6 days ago • alphaflylizard

bases from the designated span (column C) will be trimmed. So I guess my inputs could be assembly in fasta file and tsv table with transcript id and desired span to be trimmed. I see this question was asked [here][1], but it was more

RNAseq assembly transcriptome contamination

updated 6 days ago • Lada

column into umap coordinates csv file umap_ordered = NDN_index.merge(umap_cord, on = "Cell_ID") #merge based on Cell_ID umap_ordered = umap_ordered.iloc[:,1:] NDN.obsm['X_umap'] = umap_ordered.values ValueError: Value passed...of parent. Value had shape (0, 2) while it should have had (14872,). ``` I think the error is at merge step because. I am merging the data frame NDN_index with umap_cord …

RNA-velocity scanpy loomfile scvelo python

updated 6 days ago • Kash

Hi, I am planning to download datasets from ENCODE, but I am confused on when and how should I merge the replicates. For example, There is a CHIP experiment, it has H3K9me3 samples and input samples. H3K9me3 has two biological...replicates. Each technical replicate has four runs. In this case, I will download all 32 SRAs. Merge runs using cat, resulting in 8 SRAs (technical replicate …

CHIP-seq encode

updated 6 days ago • Nurken

Hello. I want to merge 7 Seurat objects and do batch correction. How can I do this? I'm going to use the merge() function to merge seurat objects. If

Seurat

updated 6 days ago • sooni

Dear all, I have a multi-fasta file which consists in 1,000 coding sequences. I would like to compute the Ka/Ks between each pair of sequences. For the...I would actually want to repeat that for many different genes, so for many different multi-fasta files each containing 1,000 sequences and sometime even more. The largest multi-fasta file I have contains 9,000 sequences

Pairwise-Alignment Genomics Ka-Ks

updated 7 days ago • maxime.policarpo

Hi im traying to get some visual summaries from a vcf i annotated with VEP, and for that i want to use maftools but firts i have to get a maf file, so i use `this comand: perl vcf2maf.pl --input-vcf /home/victor/ensembl-vep/test_ann.vcf --output-maf tests/test.maf --tumor-id TUMOUR --normal-id NORMAL --inhibit-vep.` which gives me this errors [.......] [W::fai_get_val] Reference chr10:1…

vcf vcf2maf maf maftools VEP

updated 7 days ago • Javier

and already sorted; unfortunately, Neanderthal has five BAMs which were not sorted and needed to be merged... So, I first proceeded to sort them — with `-n` to have the files ordered by read name — and then attempt to merge them with `samtools...for each tag ID. ``` After a bit of research, I though the problem could have been that sorting and merging alone would have caused this; hence, followi…

samtools bam

updated 8 days ago • Matteo Ungaro

NGS tools - we used these library kits). 4. Alignment and sort (of each splited BAMs) 5. Merge Bams of each sample. Now, I want to mark duplicates in my Bams, for which I was looking for tools. So far, I could find few tools...if using for subset of my reads, running on cluster. ![RG header of my bam][1] ![Bam file after merging (step5)][2] ![Bam file after SetMateInformation for fgbi…

Deduplication UMI

updated 8 days ago • Lipika

I want to map a FASTA sequence that spans over introns against the genome in order to get its coordinates in the GTF format. I'm using a genome...somehow could be turned into GTF format. Is there a mapper with the similar output (psl) and input (FASTA) requirements? I tried to use mappers like HISAT2 and STAR but I did not achieve my goal. The cDNA sequence (FASTA) derived...reports only the…

mapping

updated 11 days ago • rahu

many papers, at last I decided to use mirdeep2 tool.for running this tool for my research, - a FASTA file with the reference genome - a FASTA file with the reference miRBase mature miRNAs for the vigna mungo species - a FASTA...file with the reference miRBase mature miRNAs for related species - a FASTA file with the reference miRBase precursor miRNAs for the vigna mungo species - a FAST…

differential-expression mirdeep2 miRNA

updated 11 days ago • Ashok

bowtie2 to align the fastq files to a reference genome for the same bacteria I found off NCBI (the fasta file ends in .ffn) I converted the sam to bam, sorted, and indexed bam file using sam tools. I know I need to use something like

differential-expression transcriptome

updated 11 days ago • siddharth.patel.153

raw reads were then: - Demultiplexed and adepter clipped - Filtered by restriction enzyme cut site - Merged and Clusterized using CD-HIT-EST to form the reference contigs - Quality trimmed - Aligned against the reference contigs

radseq batch-effect SNP

updated 11 days ago • oselm

I have merged two RNA-seq datasets from two different batches. The problem is that the sequencing batches are perfectly collinear

RNA-seq batch-effect

updated 11 days ago • boymin2020

I'm trying to trace the gene expression dynamics upon my drug treatment. I found that if I simply merge two datasets into one master table and plot the RPKM and Fold Change values, the numbers do not reflect the real dynamics

sequence RNA-Seq RPKM Fold-Change batch-effect

updated 12 days ago • tud55122

example I want to perform a differential expression analysis between TypeB and TypeF. So I need to merge all these datasets into one. here are my questions: 1. Is it possible to merge these datasets into one? (considering I want...to perform a differential expression analysis (DEA)) 2. Should I normalize them before merging ? if yes what normalization techniques should I use? 3. How to merge…

limma microarray DEA batch-effect

updated 12 days ago • asalimih

method, SCtransform method, harmony method, which one is more suitable for my case, or I just merge six sample together directly? 2. If use Seurat integrate pipeline and SCtransform pipeline, they recommand to use "RNA

Seurat scRNA batch-effect harmony

updated 12 days ago • 623202215

behavior and avoid issues with 0/0 genotypes appearing as missing, I don't use the -v option). 2. Merging the resulting BCF files with bcftools merge 3. Filtering insertions/deletions (indels) 4. Splitting multiallelic...has a -b option that allows calling variants from a list of BAM files directly, bypassing the merging step (simulating a merged .bam file). However, the results from these two…

vcf bam bcf snps

updated 12 days ago • George

CDS (coding sequence) as a small scaffold at the end of the genome. I then want to generate a new FASTA, GFF, and transcriptome file with this update. I've tried using Geneious, but have been struggling with the gff formatting...new CDS sequence as a scaffold to an existing human genome assembly? - How can I then regenerate the FASTA, GFF, and transcriptome files to incorporate this new scaffol…

gff agat transcriptome

updated 12 days ago • LDT

patient from Mutect2 and Sanger sequencing, resulting in two versions per patient. Then, I would merge all patients into a single file. This would give me files like: step 1 E.g., `APGI-AU_DO32825_gatk-mutect2_indel_snv.vcf.gz...and SA407795 in INDEL). I am not certain how this will affect downstream analysis, or if I should merge them differently. Additionally, I am aware of tools like Sarek t…

bcftools SnpEff WGS VEP VCF

updated 12 days ago • Javier

Hi, I am trying to create a sequence table from the dereplicated FASTA files by Vsearch and run the chimera filtering by DADA2 over it. I created an OTU table with Vsearch using the commands...Hi, I am trying to create a sequence table from the dereplicated FASTA files by Vsearch and run the chimera filtering by DADA2 over it. I created an OTU table with Vsearch using the commands below: …

OTU sequencetable DADA2

updated 12 days ago • Ali

platform was calculated and subtracted from the full set of GAII data. The corrected GAII set was merged with the HiSeq data set followed by gene median centering. Is this strategy a good or bad idea, vs other techniques of

RNA-Seq batch-effect

updated 12 days ago • denalitastic

Hi everyone, I'm researching growth Differential Expression Genes (DEGs). To do this, I chose fetal , juvenile and adult ages. I found the fetal age data from the GEO site, which was prepared by microarray method and Juvenile and adult ages data from the ArrayExpress site which was prepared by rnaseq method. I calculated the expression values of the microarray and rnaseq data separately. then I …

microarray RNA-Seq batch-effect R

updated 12 days ago • Fahimeh.6868

4 scRNAseq samples that I create Seurat objects for. I do the QC on each of these samples and then I merge them using the merge function from Seurat. I then normalize, scale, and run PCA on the merged dataset. Then, I take the normalized...Seurat and input it into Harmony. Do I have to normalize and scale each sample individually before merging it and normalize it again? or do I normalize only af…

single-cell seurat batch-effect

updated 12 days ago • fouerghi20

Hi I have mapped some pacbio reads to a mammal reference and I am now focusing on understanding the coverage in a ~5Mb region of interest. It seems the majority of the region is well covered by reads. However, a locus of about 500kb in the centre of the region has no reads mapping to it at all. I have downloaded a RepeatMasker track from the UCSC and found that the 5MB region appears to be, at…

sequence RepeatMasker pacbio

updated 12 days ago • epaminonda

and finally, I want to remove the batch effect between them. I want to know if is it correct to merge these two datasets at first and then perform quality control , background correction, and normalization and then perform...quality control , background correction, and normalization separately for each dataset at first then merge these datasets and remove the batch effect

R microarray affymetrix batch-effect quality-control

updated 12 days ago • Sib

celfile.path = "Data/GSE32323/") dataset2<-ReadAffy(celfile.path = "Data/GSE8671/") gse<-merge(dataset1,dataset2) #### Background correction, Normalization, Log transform, and extraction of series matrix rma<-rma

Batch-effect microarray R

updated 12 days ago • Sib

created a PCA plot for all the samples (representing conditions A and B) from the three datasets by merging the raw counts and then doing the normalization and vst transformation using DESeq2. The plot shows that the samples

batch batch-effect DESeq2 rna-seq

updated 13 days ago • mmitra

Hello, as I am attempting to merge seurat objects following sctransformation and I am continually running into subscript out of bounds in seurat expression

Seurat SCT

updated 14 days ago • michelle.swarovski

question regarding the detection of differentially expressed genes from combined datasets. So as to merge two expression microarray datasets, following the combination of series matrices and their corresponding annotation

limma sva batch-effect R

updated 14 days ago • amirmehrgou

I encountered an error "Value was put into Pairinfo Map more than once" while running picard's MarkDuplicates on a bam file that was created by merging files from three different runs. I found several threads on Biostars addressing this issue, e.g. https://www.biostars.org/p/60263/ however, I'm not sure how and where to best implement the suggested corrections of fixing the SM tag (e.g. …

picard MarkDuplicates

updated 14 days ago • shpak.max

Hello, I work on merging GVCF files. Each sample has undergone HaplotypeCaller, and GVCF files were created by chromosome. Now, I have 24 GVCF...files per sample and I want to merge them into a single GVCF file per sample. Eventually, I am going to use GVCF files in GenomicsDBImport and then do GenotypeGVCFs...for joint calling. To merge GVCFs, some papers have done this by using MergeVcfs …

CombineGVCFs MergeVcfs GATK WGS GVCF

updated 14 days ago • prds

Hi, I assembled the genome using PacBio HiFi reads and Hi-C reads. I want to know how can I identify the gaps in genome. Is there any good tool for this? I shall be grateful to you.

awk seqkit assembly fasta genome

updated 14 days ago • rj.rezwan

cell types in each clusters by using genes expression using Seurat in R. However, it comes from merge Seurat. I want to plot a heatmap which shows genes scores for the marker genes in one expression module (one cluster) from

scRNA heatmap

updated 15 days ago • Hien

Good day, I have summary statistics of my APOBEC3 gene which were generated using `plink --assoc`. I have also used `plink --hardy` to assess deviation from hwe. Now I need to translate these summary stats into a publication ready table that shows frequency and distribution of the apobec3g genotypes and their association with HIV status. is there an R or even pandas script that I can use to do th…

PLINK PANDAS R

updated 15 days ago • Koketso

akk/software_library/CIRIquant_env/bin/samtools # Paths to reference files reference: fasta: /home/akk/hg38_genome/hg38.fa gtf: /home/akk/hg38_genome/hg38.refGene.gtf bwa_index: /home/akk/hg38_genome/hg38/hg38

ciriquant

updated 16 days ago • Atul K.

the cDNA dataset was submitted in EMBL database. I was not able to download these cDNA sequences in Fasta format from EMBL, but it worked in NCBI. here is the Accession numbers for submitted data can access in NCBI: Oryza sativa...these dataset, but it not work like my expectation. The download files are log files, not in fasta format. Here is my script: #!/bin/bash start_a…

NCBI. cDNA

updated 16 days ago • Sony

wp-content/uploads/sites/25/2014/05/Module-7.-Duplication-and-Degradation.pdf where I 1) take the FASTA nucleotide sequence for my gene of interest (as determined by the annotation of my genome) and blast (do I use blastn? or

blast duplication paralog genome

updated 17 days ago • brimaloney24

Hi, I want to replace the gene_ids with new ids of some selected genes in a large fasta file. How can I do this? old new gene_1 sg1.1 gene_10 sg10.6 gene_20 sg20.8

fasta bioawk awk seqkit

updated 17 days ago • rj.rezwan

2 VCF files (in the folder there are the two .tbi files) with following command: bcftools merge -m snps -O v -o merged.vcf a.vcf.gz b.vcf.gz but got these error : ``` [E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used

vcf tabix bcftools

updated 18 days ago • giulia.cosenza

Hi, I have a task to transfer cram file to fa file. For example, I have a cram file named as chr_123.cram. I intend to use samtools to transfer this file to fa file, with reference genome hg38.fa. The out file should be chr_123.fa. My chr_123.fa should contain chr information, for example: ``` >chr1 ........................ ``` But my current method (samtools) only uses my fa file, and my …

fasta cram genome

updated 18 days ago • me

I am using [fastp][1] for quality trimming, PE read merging and adapter trimming. However, it behaves unexpectly with regard to adapter trimming - leaving some untrimmed while

trimming fastp adapter

updated 18 days ago • liorglic

12,241 results • Page 1 of 245

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Answer: Extract protein sequence

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Comment: How to calculate identity percentage between proteins contained in a FASTA file?

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