Biostar

12,280 results • Page 2 of 246

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 22 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 22 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 23 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 23 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 23 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 24 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 25 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 27 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 27 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 27 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 27 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 27 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 28 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 28 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 28 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 28 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 28 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 28 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 28 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 29 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 29 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 29 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 29 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 29 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 29 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 29 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks ago • liorglic

this (VERY IMPERFECT) classification, I was able to assign a genotype to those cells. From there, I merged both sequencing runs into a single Seurat object with 18k cells classified by genotype: Fib4 | WT | NA ---|---|--- 7460 | 3388 | 7408 The

cell seurat single score

updated 5 weeks ago • txema.heredia

set of sample. I passed through all phases as follow: filtration, run error model, sample inference, merging, constructing ASV. My question is regarding the stage "Sample inference": My understanding is that this stage generate...getN) with getN(dadaFs) colnames(track) <- c("input", "filtered", "denoisedF", "denoisedR", "merged", "nonchim") I obtained this table: ![Table][1] Could you…

Microbiome R dada2

updated 5 weeks ago • Mohamed Samir

the proper calculation in order to find a metric equivalent to the "logFC" of limma? 3) Can this merged dataset be used in combination with the `limma` package instead of the `glm()`? I have already done this downstream analysis...The only boudt is wheter the logFC values are properly calculated (as the merged dataset contains Z-scores). In my analysis, the logFC values range from -0.7 to 0.9, w…

microarray Z-score limma differential-gene-expression meta-analysis

updated 5 weeks ago • michael.s

identify differentially expressed genes by comparing both datasets. So for this I have tried first merging both the datasets and performing differential expression using limma, then I have also tried taking ratio or gene

gene-expression R protein-expression Differential-gene-expression Volcano-plot

updated 5 weeks ago • vin23

based data analysis of gene expression data to find out potential biomarker of cancer .I have merged 3 datasets without any treatment ( two of Affymetrix Human Genome U133A Array and one with Affymetrix Human Genome

limma differential-gene-expression r

updated 5 weeks ago • 1234anjalianjali1234

levels of expression?? The pipeline could be something like: - Assembly using Trinity+Velvet+SOAP - Merge and redundancy reduction (ex. EvidentialGenes) - ORF obtention (maybe Transdecoder or other tool) - Blastx agaisnt Swissprot

differential-gene-expression RNA-Seq ORFs

updated 5 weeks ago • pablo61991

When we are working with non-model organisms and we perform our assemblies. At the end we have a .fasta file with all our transcripts which corresponds either to true transcripts and artifracts/nonsense/bad transcripts.I...checked the % of mapping, the BUSCO score and also de Transrate score, and we had our confidence .fasta file with our good transcript. What is the correct order to proceed at t…

differential-gene-expression RNA-seq

updated 5 weeks ago • pablo61991

description here][1] update: the cases are --> https://pastecode.io/s/j79ti1me Do I have to merge these files together for analysis? [1]: /media/images/769fa043-a900-4f6d-ae13-f3869760

Differential-gene-expression TCGA miRNA

updated 5 weeks ago • mohammadhassanj

donor7 <- PercentageFeatureSet(donor7, pattern = "^MT-", col.name = "percent.mt") donors <- merge(donor1, y = c(donor2, donor3, donor4, donor5, donor6, donor7)) VlnPlot(donors, features = c("nFeature_RNA", "nCount_RNA", "percent.mt

batch-correction R seurat monocle3 cds

updated 5 weeks ago • sooni

BaseSpace -- http://basespace.illumina.com - Seven Bridges Genomics -- http://www.sbgenomics.com (merged with Pierian, UgenTec into Velsera) - Pine Biotech -- http://pine-biotech.com/ - GenoSpace -- http://www.genospace.com - Cypher

cloud-genomics

updated 5 weeks ago • 14134125465346445

12,280 results • Page 2 of 246

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