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4
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5
replies
2.5k
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For high quality Telomere to telomere assemblies, is short read polishing still necessary
genome illumina sequencing nanopore wgs
updated 2.1 years ago by ★ 2.4k • written 2.1 years ago by ▴ 60
0
votes
3
replies
1.2k
views
RdRp scan - identifying/detecting viruses- metagenomic workflow- need help
RdRp virus-detection metagenomic
updated 2.0 years ago by 45k • written 2.1 years ago by • 0
0
votes
0
replies
1.1k
views
Job: Biology Assistant Professor in Bioinformatics, Agnes Scott College, Atlanta, GA
assistant-professor tenure-track
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
1
vote
2
replies
840
views
Is it possible to submit multiple MS raw data files to MASCOT as a batch
MASCOT
2.1 years ago by peter.berry • 0
0
votes
2
replies
903
views
circRNA isolation
circular-RNA circRNA cDNA
2.1 years ago by dbagmerve • 0
0
votes
9
replies
2.8k
views
Large number of gaps at the beginning of alignments
clustal-omega DNA alignment
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
2
votes
2
replies
1.5k
views
Pangenome using Orthofinder
OrthoFinder Pangenome bacteria
2.0 years ago by kirankumareripogu ▴ 10
0
votes
0
replies
1.0k
views
Job: Group Leader (Plant development and diversity) at Max-Planck institute for plant breeding research (Cologne, Germany)
MPIPZ group-leader
2.1 years ago by microfuge ★ 2.0k
5
votes
3
replies
1.2k
views
Visualisation of accessible regions in single cell atacseq data
visualization scATAC-seq single-cell
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 130
1
vote
2
replies
1.1k
views
Dotplot error: subscript out of bound
R scRNA-seq seurat
2.0 years ago by Xuhao • 0
0
votes
0
replies
649
views
assembly: purge_dups removes too much sequence
purge_dups assembly nanopore repeats plants
2.1 years ago by colindaven 8.0k
21
votes
10
replies
46k
views
6 follow
read depth using samtools
depth samtools
updated 2.1 years ago by ▴ 10 • written 6.7 years ago by ▴ 40
0
votes
7
replies
2.1k
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
updated 2.0 years ago by ★ 1.6k • written 2.1 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Confused about the GERP++ output
gerp
updated 2.1 years ago by ▴ 20 • written 2.4 years ago by • 0
8
votes
5
replies
1.9k
views
Is there a benchmark analysis for the best tool for multiome single-cell RNA+ATAC data analysis?
multiome single-cell
updated 2.1 years ago by 89k • written 2.1 years ago by ▴ 180
0
votes
1
reply
1.8k
views
what is BCFtools" f_missing" removing?
bcftools missingness f_missing
updated 2.1 years ago by 166k • written 2.1 years ago by • 0
0
votes
0
replies
567
views
Paired vs Unpaired t-test: Compositional analysis in the Human snRNA-seq data
snRNA-seq scRNA-seq analysis statistic compositional
2.1 years ago by joonhong kwon ▴ 70
0
votes
0
replies
523
views
how simply mutation annotation in R?
annotation RNA-seq Bioconductor
2.1 years ago by octpus616 ▴ 120
0
votes
2
replies
982
views
Why figure from guppy basecaller show only 1 base in each event?
basecally guppy nanopore
updated 2.1 years ago by ▴ 130 • written 3.1 years ago by • 0
5
votes
12
replies
3.8k
views
Converting custom VCF to standard VCF
VCF
2.1 years ago by avelarbio46 ▴ 30
1
vote
4
replies
1.7k
views
Finding Unique values on specific INFO field of the VCF file (dbNSFP, vep annotated multisample VCF)
bcftools filter vep vcf
2.1 years ago by avelarbio46 ▴ 30
0
votes
2
replies
1.1k
views
DESeqDataSetFromMatrix error
deseq
2.1 years ago by odi ▴ 10
2
votes
0
replies
985
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 2.1 years ago by 45k • written 2.1 years ago by 166k
0
votes
2
replies
801
views
Deseq2
Deseq2
updated 2.1 years ago by 15k • written 2.1 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Job: Position Open: Postdoctoral Research Associate Functional Genomics of circular RNAs in Alzheimer’s Disease
Postdoctoral
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
2
replies
1.4k
views
NCBI nt seqid2taxid.map
ncbi kraken2 kraken database
2.1 years ago by Gio ▴ 10
2
votes
2
replies
928
views
How to split grouping information in a single expression matrix?
scRNA-seq GEO Seurat
2.1 years ago by Xuhao • 0
0
votes
3
replies
922
views
CNV using GISTIC
CNV GISTIC
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
3
votes
5
replies
3.2k
views
Does single end sequencing sequence both strands of the original fragment?
Illumina sequencing
2.1 years ago by Steven ▴ 20
5
votes
9
replies
2.6k
views
RNA-seq for differential gene expression analysis with only one biological replicates
RNA-seq
2.1 years ago by WMA • 0
6
votes
5
replies
5.1k
views
How do I install DSSP?
biopython PDB pip DSSP
updated 2.1 years ago by ▴ 70 • written 2.1 years ago by • 0
1
vote
4
replies
1.4k
views
Split reads along the genome in my samples
DNA sequencing
2.1 years ago by paulaotero.sanchez • 0
0
votes
7
replies
2.4k
views
How to get top 10 genes expressed in a cluster ( for cell type identification)?
seurat
updated 23 months ago by ▴ 70 • written 2.1 years ago by ▴ 360
0
votes
0
replies
696
views
Issue in creating Gene Regulatory Network links using CellOracle
Python CellOracle GRN
2.1 years ago by Debashish • 0
0
votes
0
replies
714
views
Cluster files from 2018-2020 archive of PDB
PDB Structural archive database
23 months ago by yhdist ▴ 70
9
votes
3
replies
1.2k
views
Seeking a real project
thesis project
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 20
7
votes
8
replies
4.1k
views
7 follow
what is the mean of the file "*._f1.fq.gz" and "*._r2.fa.gz"
RNA-Seq
updated 2.1 years ago by ▴ 70 • written 5.4 years ago by ▴ 250
2
votes
2
replies
3.3k
views
Tools to create flanking sequences for variants based on a VCF file and reference genome.
vcf assay
updated 2.1 years ago by ▴ 10 • written 9.2 years ago by ★ 5.4k
19
votes
10
replies
3.3k
views
Forum: Pain points using commercial clouds
gpt tinybio
updated 2.1 years ago by ▴ 70 • written 2.1 years ago by ▴ 850
0
votes
4
replies
1.3k
views
Analyzing time-patterns in RNA Seq data only having results_apeglm
R sequencing
2.1 years ago by Paul • 0
0
votes
0
replies
440
views
qtlseq oserror 38
qtlseq
2.1 years ago by 지헌 • 0
0
votes
1
reply
992
views
error in topGO?
gene set topGO significant
updated 2.1 years ago by 8.9k • written 2.1 years ago by • 0
9
votes
6
replies
3.5k
views
6 follow
Forum: GTF files from Ensembl Releases 105 and 106 unsorted
Ensembl bug GTF
updated 2.1 years ago by 89k • written 2.9 years ago by ▴ 30
3
votes
5
replies
2.4k
views
News: Ensembl Release 104 and newer GTF files no longer have genes sorted by position
Ensembl GTF
updated 2.1 years ago by ▴ 150 • written 2.9 years ago by ▴ 30
1
vote
6
replies
2.3k
views
Use limma for correlation analysis of RNA-seqdata and continous trait
limma RNA-seq
updated 6 months ago by ★ 8.3k • written 2.1 years ago by • 0
0
votes
1
reply
750
views
quantifying splicing transcripts for nanopore RNAseq
RNAseq splicing nanopore
updated 2.1 years ago by 154k • written 2.1 years ago by • 0
40
votes
23
replies
29k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq genome
updated 2.1 years ago by ▴ 150 • written 7.5 years ago by ▴ 760
1
vote
4
replies
7.9k
views
How to order a gff3 file by coordinates
gff3 ordering
updated 2.1 years ago by ▴ 150 • written 7.7 years ago by ★ 5.2k
4
votes
12
replies
6.0k
views
6 follow
Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
gff3
updated 2.1 years ago by ▴ 150 • written 5.4 years ago by ★ 5.4k
1
vote
2
replies
1.3k
views
convert bed12 to sorted gtf
bed12 gtf gff awk
updated 2.0 years ago by ▴ 150 • written 3.2 years ago by • 0
121,964 results • Page 207 of 2440
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alternate allele frequency and minor allele frequency
Calculating minor allele frequency for GnomAD VCF file
Hiring FT Remote Nextflow engineer to build ML workflows for cancer genomics
Answer: Gene expression equivalent of polygenic risk score ?
A: TRF output to .gff file
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Comment: Differences between published differential gene expression results and own analy
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Answer: gnomad par region variants by benformatics 4.2k
The XX and XY counts are present on any given variants page.
Comment: Help with Ideathon by Mensur Dlakic ★ 30k
I don't see a single question here. Saying `I need your expert help in figuring out how I can make this analysis useful!` is too open-ended…
Comment: Differences between published differential gene expression results and own analy by ATpoint 89k
Please link the paper, lets see their methods. With human data it can well be that they included something like surrogate variables to damp…
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
Comment: tximport error (medianLengthOverIsoform) by rfran010 ★ 1.6k
Is it the version number in your data? e.g. ENST00000415118.1 vs ENST00000415118 could be causing the mismatch?
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
So is there any correct way for normalisation? I know limma recommends CPM via limma-voom and DESeq2 just takes in raw counts and does thei…
Comment: Gene expression equivalent of polygenic risk score ? by Picasa ▴ 690
Thanks a lot for your answer. I will check the paper.
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
If those logFCs are different, then that's a normalization issue. The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
Comment: Errors with RSEM/bowtie2 by Olivia • 0
I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
Answer: Gene expression equivalent of polygenic risk score ? by GouthamAtla 12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
Comment: ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues usin by Ben • 0
write.table(df1, "df1.txt", sep = "\t", row.names = T, col.names = T, quote = FALSE)
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
That is good confirmation. Bacl to the error message. > I don't know how to fix this, given that I already did the trimming steps. DId yo…
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
Honestly, those things shouldn't result in a considerable discrepancy. The largest difference will come from the post-processing & analysi…
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