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121,965 results • Page 210 of 2440
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2
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Extract reference and alternate SNPs for different samples
vcftools bcftools SNPs
updated 2.1 years ago by 154k • written 2.1 years ago by ▴ 350
0
votes
3
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1.4k
views
Calling large domains of signal enrichment (broad peaks) from log2,input normalized ChIP-seq data
chip-seq peak-caller normalization broad-domains
updated 2.1 years ago by ★ 1.6k • written 2.1 years ago by ▴ 40
5
votes
3
replies
2.3k
views
interpreting results from pathway analysis
RNA-seq kegg clusterprofiler GSEA pathway-analysis
updated 2.1 years ago by 45k • written 2.2 years ago by ▴ 40
1
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2
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1.3k
views
Job: Universitäts­klinikum Essen PhD position in neuroscience. Germany.
UniEssen PhD
2.1 years ago by alwayshope ▴ 40
1
vote
4
replies
1.9k
views
Joint RNA and ATAC analysis: 10x multiomic - Fragment Path
ATAC-seq multiomic signac
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 10
0
votes
3
replies
1.2k
views
Understanding the Impact of DNA Methylation on Gene Expression in Different Genomic Regions
methylation EPICarray
2.1 years ago by Irene • 0
0
votes
1
reply
659
views
Merge microbiota data
microbiota OTU
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
1
vote
1
reply
786
views
READ GROUP in GATK
Variant-calling GATK
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 160
3
votes
1
reply
778
views
Finding the raw data used to build reference genomes
reference-genome
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
3
votes
2
replies
1.2k
views
Forum: How to contribute to the next edition of Biostars Handbook
handbook
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 20
1
vote
1
reply
1.2k
views
BCFtools isec output vs BCFtools query
bcftools VCF strelka2 htslib
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 260
1
vote
1
reply
1.6k
views
UMAP graph using DimPlot pre/post integration
Harmony UMAP scRNAseq
updated 2.1 years ago by ★ 1.7k • written 2.1 years ago by ▴ 10
1
vote
2
replies
1.3k
views
Pre-filtering in DESeq2 vignette
R DESeq2
2.1 years ago by dylannicoembros • 0
2
votes
6
replies
2.4k
views
Installing ensemble VEP by running INSTALL.pl takes too long.
Ensembl VEP
updated 2.1 years ago by ★ 2.4k • written 2.1 years ago by ▴ 20
2
votes
5
replies
1.5k
views
Dowload data from password protected cloud storage
data-transfer wget rclone
updated 2.1 years ago by 22k • written 2.1 years ago by ▴ 60
0
votes
1
reply
718
views
Counting Isoforms from Sam File
Samtools
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 20
2
votes
1
reply
969
views
How to change the output reference for vg giraffe BAM output
vg BAM giraffe
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 10
0
votes
3
replies
1.3k
views
GO annotation in R using library(org.Hs.eg.db)
GO Bioconductor
2.1 years ago by Nana • 0
11
votes
6
replies
5.3k
views
Short Read Data Genome Assembly
spades genome-assembly
updated 2.1 years ago by ▴ 40 • written 2.1 years ago by ▴ 240
0
votes
0
replies
469
views
Help with single cell annotation
single-cell
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 360
0
votes
3
replies
1.1k
views
Assigning GO ids to blast hits
Linux GO blast
updated 2.0 years ago by • 0 • written 2.1 years ago by • 0
0
votes
0
replies
613
views
valid pairs to .hic
HIC
2.1 years ago by GK1610 ▴ 120
0
votes
1
reply
760
views
PAML/codeml Poxvirus dN/dS
dNdS codeml selection
updated 2.1 years ago by ▴ 570 • written 2.1 years ago by ★ 2.7k
7
votes
4
replies
1.5k
views
BAM file read stats (A/T/C/G/ins/del) for each base position
SAM BAM Nanopore JBrowse
updated 2.1 years ago by ★ 2.2k • written 2.1 years ago by ▴ 20
0
votes
0
replies
1.2k
views
Job: Bioinformatics Scientist, Omaha, USA
NE SNA DPAA
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 10
1
vote
2
replies
1.6k
views
Blog: Perform Primer to Primer comparison to see and show if the primers produced are new or 100% similar to published primers
Primers emboss needle
2.1 years ago by rohitsatyam102 ▴ 940
0
votes
3
replies
1.5k
views
Bowtie2 Error: reads file does not look like a FASTQ file
bowtie2 alignment
updated 23 months ago by 89k • written 2.1 years ago by • 0
0
votes
1
reply
799
views
Replace ambiguous characters in fasta MSA
maximum-likelihood DNA
updated 2.1 years ago by 22k • written 2.1 years ago by • 0
1
vote
1
reply
982
views
Any online course for learning how to use PLINK?
plink
updated 2.1 years ago by ★ 3.1k • written 2.1 years ago by ▴ 60
0
votes
0
replies
524
views
Reverse complement only sequences resulted from BLASTN minus
DNA fasta bash
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 30
0
votes
0
replies
565
views
Problem with BUSCO alignments: more than one set of sequences for the same locus
problem phylogenomics BUSCO alignment
2.1 years ago by silviaas • 0
1
vote
1
reply
682
views
First genomic coordinate that Nanopore read aligns to
BAM
updated 2.1 years ago by 154k • written 2.1 years ago by • 0
8
votes
4
replies
2.8k
views
How to remove the gene label in heatmap RNA-seq
complexheatmap
2.1 years ago by Chris ▴ 360
0
votes
0
replies
508
views
How to compare degradation rate or half-life
degradation-rate half-life
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
2
replies
810
views
I am interested in creating bar graphs from the outcomes of my BLAST analysis
Blastn
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 40
4
votes
0
replies
1.0k
views
Herald: The Biostar Herald for Wednesday, September 06, 2023
herald
2.1 years ago by Biostar 3.6k
0
votes
0
replies
630
views
OrthoPhy
orthophy orthofinder
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 40
1
vote
4
replies
1.1k
views
Gene expression
RNA-seq DESeq2 Heatmap
updated 2.1 years ago by 89k • written 2.1 years ago by • 0
0
votes
0
replies
749
views
Job: Austria: Assistant Professor (tenure-track) and Professor (tenured) positions in Data Science
data-science statistics
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 10
2
votes
2
replies
4.5k
views
Insert size is so small, good or bad?
Insert-size RNA-Seq
updated 2.1 years ago by 45k • written 7.9 years ago by ▴ 180
0
votes
0
replies
362
views
Molecular Docking, Sars-cov-2
Molecular-docking
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
0
replies
561
views
How to assemble bacterial genomes accounting for plasmids?
genome assembly bacteria
2.1 years ago by marongiu.luigi ▴ 760
3
votes
2
replies
3.0k
views
Extracting Residuals from Differential Expression Model
statistics residuals limma
updated 2.1 years ago by ★ 8.3k • written 6.2 years ago by ▴ 250
0
votes
1
reply
641
views
Alignment of things other than DNA or Protein Sequences
alignment
updated 2.1 years ago by ★ 30k • written 2.1 years ago by • 0
3
votes
5
replies
2.1k
views
Ensembl site unresponsive in clusterProfiler analyses
parallell clusterProfiler R
updated 2.1 years ago by ▴ 570 • written 2.1 years ago by • 0
2
votes
4
replies
1.8k
views
Database for cell lines, genes and proteins associated with them
proteomics cell-line
updated 2.1 years ago by ▴ 140 • written 2.2 years ago by ▴ 40
0
votes
1
reply
699
views
IPYRAD - Step 3
IPYRAD
updated 2.1 years ago by 166k • written 2.1 years ago by • 0
1
vote
5
replies
1.5k
views
GRCh37/38 reference genotype AF wrong ?
GRCh38 reference-genome variant
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
3
votes
3
replies
1.4k
views
How to find variants in a specific gene in a cohort of 500k+ individuals?
variants plink SNPs CNV
updated 2.1 years ago by 166k • written 2.1 years ago by ▴ 60
5
votes
2
replies
1.3k
views
samtools ampliconclip option --strand is not working?
samtools ampliconclip
updated 7 months ago by ▴ 50 • written 2.1 years ago by ▴ 110
121,965 results • Page 210 of 2440
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Comment: Getting just fastqc.zip file?
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
A: GATK ASEReadCounter: Downstream analysis for identifying allele specific express
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Recent Replies
Comment: Help with Ideathon by V K • 0
Thank you for the response! Unfortunately this is completely independent and not part of a course. I was asking for some innovative ways to…
Answer: How to create a consensus of a contig with samtools or bbmap? by lieven.sterck 16k
You assembled a genome using samtools ???? that sounds very weird, if not impossible ... The header (SQ lines) is missing from your file b…
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)
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