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121,961 results • Page 185 of 2440
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3
votes
2
replies
1.4k
views
Samtools index not working in Snakemake
snakemake samtools
updated 23 months ago by 13k • written 23 months ago by ▴ 210
2
votes
1
reply
1.0k
views
Do threads matter for host DNA removal with bbmap?
bbmap metagenomics
updated 23 months ago by 45k • written 23 months ago by ▴ 10
6
votes
2
replies
950
views
Database of Mapped Data for Single Cell Sequencing
Database single-cell
updated 23 months ago by 154k • written 23 months ago by ▴ 20
3
votes
7
replies
2.3k
views
IGV not showing bigwig track information
bigwig IGV ChIP-seq
updated 22 months ago by 89k • written 23 months ago by ▴ 10
0
votes
1
reply
865
views
Perform PCA
plink
updated 23 months ago by ★ 3.1k • written 23 months ago by • 0
1
vote
0
replies
860
views
Job: Postdoctoral Fellow/Researcher in Computational Biology & Gene Regulation, Norway
deep-learning
updated 23 months ago by 45k • written 23 months ago by ▴ 910
4
votes
8
replies
2.4k
views
STAR paired-end sequencing: Both reads of the pair map when I map as single-end, but not when I map them as paired end
-seq STAR RNA
updated 23 months ago by 154k • written 23 months ago by • 0
2
votes
10
replies
2.7k
views
cellranger count matrix
count-matrix cellranger
updated 23 months ago by 89k • written 2.3 years ago by • 0
3
votes
1
reply
1.0k
views
How will you perform batch correction in DESeq2 when you don't have any group information?
batch-correction DESeq2
updated 23 months ago by 45k • written 23 months ago by ★ 4.4k
1
vote
4
replies
2.2k
views
scRNA-seq quality control
qc scrnaseq
updated 22 months ago by ★ 1.9k • written 23 months ago by ▴ 130
0
votes
0
replies
737
views
Trouble Adding Log Fold Changes to KEGG Pathway Visualization
KEGG RStudio
updated 22 months ago by 45k • written 23 months ago by • 0
3
votes
3
replies
1.3k
views
CombineGVCFs skips a chromosome
CombineGVCFs gatk
updated 23 months ago by 154k • written 23 months ago by ▴ 10
0
votes
6
replies
2.0k
views
Help locating TCGA data from cbioportal
cancer TCGA RNA cbioportal CNA
22 months ago by ConvolutedGenome ▴ 60
0
votes
0
replies
534
views
Identification of metabolites via spectral library search?
search metabolomics library spectrum
23 months ago by huynguyen96.dnu ▴ 50
0
votes
2
replies
1.5k
views
kraken2 database error: `No preliminary seqid/taxid mapping files found, aborting.`
installation kraken2 metagenomics
updated 14 months ago by ▴ 80 • written 23 months ago by ▴ 10
2
votes
14
replies
3.3k
views
How to slice a CRAM file into the 50kb regions padded with 1kb?
GATK BED CRAM WGS
updated 23 months ago by 89k • written 23 months ago by • 0
0
votes
0
replies
565
views
filtering SNV/INDEL in tumor-only WGS samples
Tumor-only samples
23 months ago by Bogdan ★ 1.4k
0
votes
1
reply
1.2k
views
WGCNA
WGCNA p-value
updated 23 months ago by ★ 1.9k • written 23 months ago by • 0
3
votes
9
replies
5.2k
views
kraken2 database does not contain necessary file taxo.k2d
shotgun metagenomics kraken kraken2
23 months ago by 10mz1 ▴ 10
3
votes
4
replies
1.6k
views
Why am I getting different results with kallisto?
kallisto
23 months ago by bioinfo ▴ 160
5
votes
8
replies
1.8k
views
duplicates issues when trying to convert long to wide in R
R
23 months ago by happyday1661 • 0
2
votes
1
reply
983
views
Job: Postdoctoral Fellow in Computational Biology, USA
cfDNA epigenomics
updated 23 months ago by 8.0k • written 23 months ago by ▴ 10
2
votes
8
replies
2.2k
views
In VEP annotation, how is the codon field interpreted?
ensembl codon vep protein
22 months ago by Atefeh ▴ 10
0
votes
9
replies
1.9k
views
Detect contaminating organism
contamination taxonomy BLAST
updated 23 months ago by 20k • written 23 months ago by • 0
0
votes
6
replies
1.5k
views
Add braces to the DNA sequence for re quested primer position.
python subprocess
updated 22 months ago by 45k • written 23 months ago by • 0
0
votes
1
reply
778
views
Linking promoter regions to genes - a database?
promoter gene-expression
updated 23 months ago by 154k • written 23 months ago by ▴ 120
0
votes
3
replies
1.9k
views
Why do we remove multi-allele when conducting a GWAS or NGS-sequencing analysis?
NGS multi-allele GWAS
updated 23 months ago by ▴ 10 • written 23 months ago by • 0
0
votes
0
replies
537
views
additive genetic variance
genetics
23 months ago by unepanthere056 • 0
1
vote
6
replies
3.0k
views
Nextflow bwa-mem2 pipeline/channel question
bwa-mem2 bwa nextflow
23 months ago by megaphonecat ▴ 10
0
votes
0
replies
577
views
best annotator for mitochondria and heteroplasmy calculation
heteroplasmia mitochondria annotation mtDNA
23 months ago by toma.85 • 0
0
votes
1
reply
836
views
How to make an amino acid sequence using `AAString ()`?
String geom_seqlogo ggplot2 R ggmsa
updated 23 months ago by 13k • written 23 months ago by ▴ 350
0
votes
2
replies
933
views
phylogeny analysis
27
updated 23 months ago by 45k • written 23 months ago by • 0
0
votes
3
replies
1.4k
views
BAM file for phasing
imputation GATK phasing Beagle
updated 22 months ago by ★ 3.1k • written 23 months ago by • 0
3
votes
3
replies
2.0k
views
RNA-Seq with DNA contamination, any way to salvage the data?
contamination RNA-Seq DNA
updated 23 months ago by 89k • written 23 months ago by ▴ 20
1
vote
3
replies
1.2k
views
Merge or integrate multiple samples and then do downstream analysis
Seurat
updated 23 months ago by 89k • written 23 months ago by ▴ 20
1
vote
1
reply
1.4k
views
Kaiju database download
kaiju RAM database
updated 23 months ago by ★ 1.2k • written 23 months ago by ▴ 10
0
votes
1
reply
1.2k
views
Comparative transcriptomics between species
Transcriptomics rna-seq
updated 23 months ago by ★ 1.2k • written 23 months ago by • 0
0
votes
0
replies
1.3k
views
Diffbind: can not load file Error in if ((length(callers) == 1) & (callers[1] == "counts")) { : argument is of length zero
Diffbind
23 months ago by makwana.kd ▴ 60
5
votes
8
replies
2.1k
views
UCSC custom track upload direct data POST / without url
api ucsc
updated 22 months ago by ★ 1.8k • written 23 months ago by ▴ 10
2
votes
3
replies
1.1k
views
Options for assigning cell labels to barcodes from CITE-seq experiment
single-cell
23 months ago by Chris Dean ▴ 420
5
votes
5
replies
1.5k
views
6 follow
Finding exons that are always included
alternative-splicing exon
updated 23 months ago by 23k • written 23 months ago by ▴ 50
4
votes
4
replies
1.6k
views
Extract of no. shared gene names in disease-disease association though API from Disgenet Database
Gene-Disease-Association API Disgenet Disease-Disease-Association
23 months ago by alirejwan.stars1994 • 0
0
votes
1
reply
993
views
qiime2 paired end fastqs import
qiime2 metagenomics
updated 23 months ago by 154k • written 23 months ago by ▴ 10
0
votes
0
replies
460
views
Metabric expression data through CbioPortal
cBioPortal Metabric
23 months ago by Tom • 0
4
votes
7
replies
1.7k
views
SNP IDs
SNP
22 months ago by kl ▴ 20
3
votes
6
replies
3.3k
views
kraken2 bacteria database 250GB+
metagenomics 16s kraken2 kraken
updated 10 months ago by ▴ 20 • written 23 months ago by ▴ 10
1
vote
9
replies
2.0k
views
Command line or python RNA-seq read simulator
simulation RNA-seq
23 months ago by i.sudbery 22k
1
vote
0
replies
1.2k
views
Job: Bioinformatics Research Associate, Genomics and Genetics at Vanderbilt University, USA
Genomics Genetics
updated 23 months ago by 8.0k • written 23 months ago by ▴ 30
1
vote
0
replies
1.2k
views
Job: Bioinformatics Research Associate in Transcriptomics, Epigenomics and Multi-omics
Transcriptomics multi-omics Epigenomics
23 months ago by JP ▴ 30
0
votes
2
replies
810
views
biomaRt Ensembl version 83 (mouse)
Ensembl biomaRt
updated 23 months ago by 45k • written 23 months ago by • 0
121,961 results • Page 185 of 2440
Recent Votes
A: Which is the proper RNA-seq count table transformation to perform hierarchial cl
Answer: Differences between published differential gene expression results and own analy
Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
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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…
Answer: Differences between published differential gene expression results and own analy by Ales ▴ 50
I second the comment about comparing the top 100 genes - if you see vastly different results, I would lean closer to examining protocols th…
Answer: Help interpreting BLASTn results and phylogenetic tree for genetics practical by Mensur Dlakic ★ 30k
I think what you are asking involves too much work for anyone to explain it in granular detail. But who knows, maybe there is a good soul o…
Answer: Differences between published differential gene expression results and own analy by yura.grabovska ▴ 830
When you say vastly different, what do you mean exactly? Does your top 100 up/down not match theirs at all?
Comment: Functional prediction for proteins of bacteria. by colindaven 8.0k
Have a look at tools like SnpEff or Ensembl VEP. Perhaps your bacterial sp is included.
Comment: Errors with RSEM/bowtie2 by Olivia • 0
Yes, I already made the transcriptome with these tools, and the CD-HIT-EST fasta file is the transcript file that I am using for RSEM. Then…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks by Guilherme • 0
Oh, ok. It seems like NCBI stores the files in SRA format (thus needing conversion and database lookups by sra toolkit tools) and EBI store…
Comment: help with modkit on nanopore sequencing data. by andres.firrincieli 3.9k
On the DMR tutorial page, they retrieve Human CpG Islands from the UCSC Table Browser. You can do the same thing for Mouse CpG Islands. Hav…
Comment: After doublet detection in 10x scRNA-Seq data, there is still evidence of double by yura.grabovska ▴ 830
Yes but the problem is that biological knowledge is never fully encompasing. While I can say that a cell expressing CD45 alongside astrocyt…
Comment: DNA copy number blacklist for excluding common unreliable regions by yura.grabovska ▴ 830
Human genome, ideally hg38
Comment: Is Newbler still available for download by anweshaash • 0
Hello, I am wondering if you got access to the software or not. I am looking to use Newbler for my research and I contacted Roche too but t…
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
> I have previously run Trinity with the Trimmomatic step as well as CD-HIT-EST. I assume you did the above to generate the transcriptome,…
Answer: With 10x Visum HD : How to map the barcode id to the barcode sequence ? by sacha ★ 2.5k
Got it https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-inclusion-list-formerly-barcode-whitelist
Comment: limmaFit error when comparing TCGA RNA-Seq data by vernonlim98 • 0
Thanks for the advice. Am still new to RNA seq and R programming in general, and will just do the analysis by myself.
Answer: The Biostar Handbook. A bioinformatics e-book for beginners. by Istvan Albert 103k
Update as of **August 2025**: The book now includes a new online course: [**FastTrack Bioinformatics 2025**][course] at no extra cost. Bio…
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