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122,198 results • Page 632 of 2444
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How to create a proper design matrix/contrast matrix for methylation 850k analysis in limma?
850k methylation analysis R limma design matrix
updated 4.4 years ago by • 0 • written 5.8 years ago by ▴ 140
2
votes
5
replies
4.8k
views
Snakemake error: "Removing output files of failed job since they might be corrupted:"
Snakemake
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 100
2
votes
5
replies
5.7k
views
Beagle: Skip intervals with no common markers
beagle plink vcf conformgt
updated 4.4 years ago by ▴ 20 • written 5.8 years ago by ▴ 10
1
vote
0
replies
735
views
Duplicate genotypes after phasing in Beagle
Beagle Phasing
4.4 years ago by PKW ▴ 110
1
vote
0
replies
1.2k
views
Deeptools plotPCA on RNA-seq help
PCA deeptools RNAseq
4.4 years ago by jrichardalbert ▴ 10
1
vote
2
replies
1.3k
views
How to perform differential expression on proteomics data?
proteomics TMT Differential-Expression R
4.4 years ago by lenC_biotecLover ▴ 90
2
votes
6
replies
3.6k
views
How to find overlapping coordinates of a gtf file
gtf-file sequencing genome annotation RNA-Seq
updated 4.4 years ago by 36k • written 4.4 years ago by ▴ 320
0
votes
4
replies
1.7k
views
how to merge two files in two columns using bash command lines
assembly fasta trinity
updated 4.4 years ago by ▴ 410 • written 4.4 years ago by ▴ 20
0
votes
0
replies
751
views
Series Matrix File in GEO
GEO labeling GEO2R
4.4 years ago by Sonia • 0
2
votes
2
replies
1.2k
views
merging fasta sequences into a single fasta sequence in large file
fasta sequences
updated 4.4 years ago by 56k • written 4.4 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Request for feature addition to p3_in.pl to extract specified length of flanking sequence around a SSR form MISA output file (genome.misa)
Primer3 ssr MISA Flanking Sequence
updated 3.9 years ago by ▴ 60 • written 4.4 years ago by • 0
6
votes
6
replies
1.8k
views
Divide by a specified member in a group in R
R dplyr
updated 4.4 years ago by ★ 2.9k • written 4.4 years ago by ▴ 700
4
votes
12
replies
2.8k
views
RNAseq analysis for aspergillus niger ?
aspergillus niger RNAseq
4.4 years ago by najibveto ▴ 130
0
votes
0
replies
621
views
Mutation rate of repeat elements
transposable mutation rate evolution elements repeat
4.4 years ago by kanamori.shunsuke • 0
0
votes
6
replies
2.4k
views
Creating Annotation GTF/GFF file
HG38 Annotation Rna-Seq Genome
updated 4.4 years ago by ★ 2.2k • written 4.4 years ago by ▴ 40
0
votes
2
replies
1.8k
views
RepeatMasker sequence identifier error
RepeatMasker
updated 4.3 years ago by ▴ 40 • written 4.4 years ago by • 0
0
votes
5
replies
1.7k
views
Create BED- or GVCF-type file for human genome
GRCh37 FASTA GVCF VCF hg19
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 250
1
vote
5
replies
2.7k
views
conform-gt error "Non-unique marker ID: ."
conform-gt error
updated 4.3 years ago by ▴ 20 • written 4.4 years ago by ▴ 20
0
votes
0
replies
724
views
map miRNA to chromosomal locations
python miRNA R location chromosome
4.4 years ago by ehruan ▴ 10
1
vote
2
replies
1.2k
views
How to calculate the difference between the RNA-Seq individual samples?
comparison expression edgeR replicates R
4.4 years ago by mohammedtoufiq91 ▴ 270
0
votes
0
replies
890
views
Job: Research assistants or postdoctoral fellows in computational biology/bioinformatics (UMass Medical School, Worcester, Massachusetts)
computational sequencing genetics genomics
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 10
1
vote
1
reply
807
views
any way to use RNA seq mapping to choose between competing gene models?
gene rnaseq prediction
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 40
2
votes
4
replies
3.2k
views
Issue with bcftools csq phasing
phasing genotyping
updated 4.4 years ago by ▴ 10 • written 7.1 years ago by ▴ 140
1
vote
2
replies
1.1k
views
fpkm values mismatch
rna topmed seq fpkm
4.4 years ago by ranjits • 0
0
votes
2
replies
1.1k
views
Comparing two highly similar genomes
genome alignment
updated 2.4 years ago by 45k • written 4.4 years ago by ★ 1.9k
0
votes
0
replies
843
views
News: Parallel bioinformatics using the GO programming language
golang parallel
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
0
votes
0
replies
633
views
How to analyse RNA-based protein pulldown mass spectrometry data
proteomics R maxquant limma
4.4 years ago by PK ▴ 130
3
votes
3
replies
2.5k
views
Bcftools isec output only contains one sample name - how to identify which samples share the same variants
bcftools vcf isec
updated 4.4 years ago by ★ 90k • written 4.4 years ago by ▴ 80
1
vote
1
reply
1.1k
views
What tools are best for conjoined gene/readthough detection and how do they differ from fusion gene detection?
conjoined fusion gene
updated 4.4 years ago by 48k • written 4.4 years ago by 23k
2
votes
3
replies
1.4k
views
Retrieving the corresponding Haplotype CDS from Ensembl
gene Ensembl protein Haplotype
updated 4.4 years ago by 24k • written 4.4 years ago by ★ 3.0k
0
votes
0
replies
751
views
RNA-Seq featureCounts Results Annotation File
Nanopore HG38 Rna-Seq Genome
4.4 years ago by santos48 ▴ 40
1
vote
1
reply
1.5k
views
What happens to the genotype field in a g.vcf after CombineGVCFs
GT GATK CombineGVCFs genotype
updated 4.4 years ago by ▴ 20 • written 4.6 years ago by ▴ 420
3
votes
0
replies
1.0k
views
News: Unix / scripting / research computing resource
scripting parallel hpc unix programming
4.4 years ago by bacon4000 ▴ 80
4
votes
9
replies
11k
views
How to find Standard Error (SE) values when not provided in GWAS summary stats?
meta-analysis gwas metal plink Standard error
updated 4.2 years ago by • 0 • written 5.6 years ago by • 0
4
votes
7
replies
3.2k
views
can't run Aracne -- Java error
aracne RNA-Seq network
updated 4.4 years ago by ▴ 740 • written 5.3 years ago by ▴ 750
2
votes
3
replies
1.5k
views
Assembly of three biological replicated metagenomics data
Assembly metagenomics analysis replicate statistics
updated 4.4 years ago by 3.9k • written 4.4 years ago by • 0
4
votes
7
replies
2.9k
views
Should we keep only the uniquely mapped reads for gene expression
RNA-seq
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 750
0
votes
2
replies
1.8k
views
Plotting residuals for limma lmfit model
linearregression limma normality residuals
4.4 years ago by ritz ▴ 10
0
votes
7
replies
3.3k
views
What are the input files for lwaldron / metaphlanToPhyloseq.R ?
r metagenomics metaphlan
updated 4.4 years ago by • 0 • written 5.3 years ago by ▴ 60
0
votes
1
reply
667
views
blastn for global alignment
global BLAST alignment
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
0
votes
2
replies
805
views
Default number of mismatches in bowtie -v alignment mode?
bowtie
4.4 years ago by lbro • 0
0
votes
3
replies
1.7k
views
samtools depth -r
WGS
4.4 years ago by lz1903 ▴ 10
0
votes
3
replies
1.9k
views
compilation terminated when R package installation in linux without superuser permission
r spp bzlib
4.4 years ago by whaiyu06 ▴ 80
14
votes
4
replies
1.8k
views
How to select columns from a dataframe of which the name ends with a specific word
R
updated 4.4 years ago by 12k • written 4.4 years ago by ▴ 20
2
votes
2
replies
1.3k
views
BWA aln, according to GDC DNA Seq Analysis Pipeline
scores BWA quality GDC Alignment
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by ▴ 10
2
votes
5
replies
2.0k
views
To retrieve the transcript from gff file with the longest isoform
isoform gff
4.4 years ago by Aneesha • 0
0
votes
2
replies
1.2k
views
Trouble with alignment using STAR - unknown error
RNA-seq alignment STAR
4.4 years ago by foxiw ▴ 10
2
votes
0
replies
840
views
How to integrate two Seurat objects
scRNA-seq Seurat
4.4 years ago by zizigolu ★ 4.4k
0
votes
1
reply
1.2k
views
Circular plot for RNA seq - methylation data
methylome plot rnaseq
updated 4.4 years ago by ★ 3.1k • written 4.4 years ago by ▴ 10
1
vote
2
replies
979
views
How does Belvu calculate conservation scores?
Conservation Belvu
4.4 years ago by jmungar2 ▴ 10
122,198 results • Page 632 of 2444
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Answer: Midpoint rooting IQTREE newick file moves node support around
Answer: Subsetting before QC in Spatial Transcriptomics
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Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
Comment: ID unifiying across different datasets
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Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by michael.ante ★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome? by dthorbur ★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
Comment: How to improving 2-Nucleotide RNA-seq Mapping Accuracy by 2411110159 • 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies by 2411110159 • 0
Very helpful!
Comment: direct RNA long-reads alignment against reference genome by frarodmar17 • 0
Okay, thanks! I removed reads.fa and I used the index created with minimap2 in .mmi format. Is this correct?
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