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121,962 results • Page 196 of 2440
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1
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5
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1.6k
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Why 99% coverage at 20X depth for sequencing?
Statistics Sequencing
updated 23 months ago by 103k • written 23 months ago by • 0
1
vote
1
reply
798
views
Clustal omega does not align: Killedssive alignment output
sequence-alignment clustal
updated 23 months ago by 45k • written 23 months ago by ▴ 760
4
votes
2
replies
1.6k
views
Visualization package for Maf Files using Python
Python maftools Visualization MAF
updated 23 months ago by ★ 1.7k • written 23 months ago by ▴ 110
8
votes
12
replies
2.8k
views
Annotating Proteins in heatmap with 1 or more pathways using R.
R Heatmap pheatmap
updated 23 months ago by ★ 1.7k • written 23 months ago by ▴ 10
1
vote
3
replies
1.6k
views
Quantify gene expression from CRAM file
Hartwig RNA-Seq CRAM
23 months ago by wenbinm ▴ 40
3
votes
5
replies
10k
views
Code for reading h5ad files in R
r RNA-seq single-cell
updated 23 months ago by ★ 1.7k • written 23 months ago by ▴ 200
2
votes
6
replies
1.8k
views
different sample size between TCGA portal and TCGAbiolinks package
mutation tcga tcgabiolinks
updated 23 months ago by ★ 1.3k • written 24 months ago by ▴ 10
2
votes
4
replies
2.0k
views
How to annotate function of genes from non-model organism
gene annotation
updated 23 months ago by ▴ 80 • written 23 months ago by ▴ 50
6
votes
4
replies
1.7k
views
Unable to install Kmergenie
sofware-error kmergenie
updated 23 months ago by 13k • written 23 months ago by ▴ 10
1
vote
6
replies
1.9k
views
error in kmergenie compilation
ntcard kmergenie
updated 23 months ago by 154k • written 3.2 years ago by ▴ 50
0
votes
1
reply
648
views
machine learning
image analysis offtopic
updated 23 months ago by 45k • written 23 months ago by • 0
0
votes
0
replies
548
views
ChIPseq gapped and braod peaks file are empty
ChIPseq broadpeak gapped peak
24 months ago by Mehvi khan • 0
5
votes
3
replies
5.2k
views
How to align multiple Sequences with one reference sequence?
alignment
updated 23 months ago by 45k • written 24 months ago by ▴ 10
3
votes
5
replies
1.8k
views
Differential gene score in single cell experiment
single-cell
updated 23 months ago by ▴ 250 • written 24 months ago by 6.5k
0
votes
5
replies
2.3k
views
Allele frequncies in plink including physical position in the output
plink vcf
updated 24 months ago by 11k • written 24 months ago by ▴ 30
5
votes
7
replies
4.1k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP genome sequence
updated 24 months ago by 103k • written 7.3 years ago by ▴ 10
1
vote
2
replies
1.2k
views
Aspiring Bioinformatics Analyst from Canada: Seeking Career Insights
career education analyst industry
23 months ago by Alex Gillard ▴ 10
0
votes
0
replies
805
views
Job: Postdoctoral Research Fellowship Program at the American Museum of Natural History
Postdoctoral-Research-Fellow
updated 24 months ago by 45k • written 24 months ago by ▴ 20
0
votes
0
replies
690
views
Job: Postdoctoral Research Fellowship Program at the American Museum of Natural History
Postdoctoral-Research-Fellow
updated 24 months ago by 45k • written 24 months ago by ▴ 20
0
votes
1
reply
936
views
Interpretation question regarding vg call result vcf
vg
updated 24 months ago by ▴ 760 • written 24 months ago by • 0
1
vote
3
replies
1.3k
views
Most sensible way to find private SNPs from a multisamples vcf with bcftools
bcftools SNP vcf
24 months ago by Axzd ▴ 80
0
votes
5
replies
2.0k
views
How long should the AAA... sequence be at the end of read, so that fastqc and multiqc consider it as poly- tail
multiqc fastqc polyA
updated 24 months ago by 23k • written 24 months ago by ▴ 50
12
votes
4
replies
2.2k
views
Tool: BBTools 39.03 released!
BBTools BBMap
23 months ago by Brian Bushnell 20k
20
votes
29
replies
5.9k
views
6 follow
Using bcftools to find unique alt homozygous sites
bcftools
updated 24 months ago by 166k • written 24 months ago by ▴ 80
0
votes
0
replies
546
views
Different colors for different features in IGV
igv color
24 months ago by mark.rose ▴ 50
0
votes
4
replies
2.4k
views
Cannot read non-existent file: when executing MarkDuplicates in a script
GATK4
updated 24 months ago by • 0 • written 3.5 years ago by ▴ 110
0
votes
1
reply
836
views
CITE-seq data visualization
immunology scRNAseq FACS 10x CITE-seq
updated 24 months ago by ▴ 150 • written 24 months ago by ▴ 40
2
votes
3
replies
1.6k
views
BioPython BLAST unusable?
NCBI blastn BioPython API BLAST
23 months ago by John ▴ 10
1
vote
3
replies
1.1k
views
GEO Dataset: Difficulty Understanding Matrices, Compliation
GEO scRNA-Seq
updated 24 months ago by 89k • written 24 months ago by • 0
5
votes
7
replies
1.7k
views
Novel disease mechanism papers from RNA-seq
RNA-seq
updated 24 months ago by 154k • written 24 months ago by ▴ 360
0
votes
3
replies
1.3k
views
Download NCBI data using sratoolkit in anaconda
NCBI sratoolkit anaconda
updated 24 months ago by 45k • written 24 months ago by ▴ 20
0
votes
0
replies
440
views
How is the ABQ field in the VCF file calculated?
ABQ VCF
24 months ago by brunomoda • 0
0
votes
0
replies
466
views
What is the waiting time to get KOBAS annotation results?
KOBAS
24 months ago by Nipan • 0
3
votes
7
replies
2.0k
views
Adapters finder
minion denovo adapters
updated 24 months ago by 154k • written 24 months ago by • 0
0
votes
0
replies
504
views
ssGSEA most differentially expressed pathways
GSVA ssGSEA
24 months ago by Hamza ▴ 10
1
vote
2
replies
961
views
Edit fasta header for TSA submission
NCBI fasta unix TSA RNA
updated 24 months ago by 154k • written 24 months ago by • 0
0
votes
2
replies
1.2k
views
Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
metagenomics metabolism humann biobakery metatranscriptomics
24 months ago by O.rka ▴ 750
0
votes
0
replies
616
views
Retrieving rs IDs from chromosome, position, and alleles
SNP GWAS
24 months ago by Jaehyun ▴ 10
6
votes
4
replies
4.2k
views
single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA
RNA-Seq
24 months ago by DrAcula ▴ 140
0
votes
1
reply
915
views
Monocle3 garnett
monocle3 garnett
updated 24 months ago by ★ 1.7k • written 24 months ago by ▴ 10
0
votes
5
replies
1.4k
views
how to assign chromosome-level annotation to a genome organised by contig?
vcftools
updated 24 months ago by ★ 3.1k • written 24 months ago by • 0
0
votes
5
replies
2.2k
views
What is the new Entrez login for NCBI API?
Entrez
updated 24 months ago by ★ 1.4k • written 24 months ago by ▴ 60
0
votes
2
replies
875
views
NIST MS Search and results
NIST Mass-Spectrometry Metabolomics
24 months ago by CECEL • 0
5
votes
12
replies
3.0k
views
sam format in the emboss water program
emboss alignment sam water
updated 23 months ago by 3.1k • written 24 months ago by ★ 1.5k
2
votes
3
replies
1.3k
views
Finding exactly where reads map from SAM
alignment read Bowtie SAM BWA
updated 24 months ago by 103k • written 24 months ago by • 0
0
votes
0
replies
804
views
Job: Postdocs and postback positions in Neuroepigenomics and psychiatric at Yale
Neurogenomics Yale Postdoc Graduate
24 months ago by alwayshope ▴ 40
1
vote
2
replies
5.4k
views
Seurat changing order cluster shown in the violin plot
R violin Seurat
24 months ago by camillab. ▴ 160
1
vote
2
replies
973
views
Filter vcf SNPs by sample GT value
bcftools variant-calling snp
updated 24 months ago by ▴ 80 • written 2.0 years ago by • 0
1
vote
3
replies
1.2k
views
bedtools: coordinates of read covered
bedtools
updated 24 months ago by ▴ 10 • written 24 months ago by ▴ 40
0
votes
0
replies
504
views
How to adjust scale on velocity plots
python
24 months ago by Chironex ▴ 50
121,962 results • Page 196 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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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…
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,…
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