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1,000 results • Page 4 of 20
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4
votes
3
replies
1.0k
views
What is the difference between vst and rlog to perform PCA ?
rlog PCA vsd
updated 11 months ago by 82k • written 11 months ago by ▴ 160
4
votes
5
replies
1.2k
views
tranfering sam file easy and fast way
SAM RNA-seq hisat2
updated 8 months ago by 43k • written 2.3 years ago by • 0
4
votes
11
replies
656
views
Remove X in row name with only number
GSVA
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 260
4
votes
3
replies
703
views
How to interpret output of PLINK association test (--assoc)
assoc
updated 8 months ago by 11k • written 8 months ago by ▴ 10
4
votes
3
replies
395
views
Single cell analysis of Cancer
cancer single-cell RNA-seq
updated 11 weeks ago by 141k • written 11 weeks ago by ▴ 20
4
votes
7
replies
819
views
SNP IDs
SNP
5 months ago by kl ▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
1 day ago by anna ▴ 20
4
votes
5
replies
539
views
Which refseq_protein db to choose for zingiberaceae
local blastp blast
updated 8 months ago by 141k • written 8 months ago by • 0
4
votes
16
replies
984
views
hisat2 location does not exist
hisat2
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
4
votes
2
replies
239
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa samtools mapping genome
updated 26 days ago by 161k • written 26 days ago by • 0
4
votes
2
replies
2.2k
views
Bfast Match Paired End Reads - Reports Half Total Number Of Reads
paired-end alignment next-gen
updated 10 months ago by 43k • written 11.3 years ago by ▴ 50
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny genome alignment
updated 11 months ago by 43k • written 4.9 years ago by ▴ 120
4
votes
4
replies
803
views
Segmentation fault Biopython pairwise alignment
biopython alignment
updated 11 months ago by 21k • written 11 months ago by ▴ 20
4
votes
9
replies
585
views
variant calling
variant-calling
updated 27 days ago by 43k • written 28 days ago by • 0
4
votes
1
reply
1.7k
views
How does FindNeighbors() and FindClusters() related and work?
seurat clustering
updated 8 months ago by ★ 2.4k • written 8 months ago by ▴ 120
4
votes
5
replies
789
views
Does adding reads cause batch effects?
kallisto RNAseq
10 months ago by bioinfo ▴ 150
4
votes
8
replies
1.9k
views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE …
super-enhancers Enhancers
updated 3 months ago by ★ 16k • written 3 months ago by • 0
4
votes
2
replies
474
views
KEGG DATABASE
DATABASE KEGG
updated 4 months ago by ★ 1.8k • written 5 months ago by • 0
4
votes
12
replies
7.8k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 11 weeks ago by ▴ 10 • written 3.4 years ago by ▴ 60
4
votes
4
replies
853
views
retaining only the clusters of interest
seurat single-cell scRna-seq
updated 10 months ago by 43k • written 10 months ago by • 0
4
votes
6
replies
2.4k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 11 months ago by • 0 • written 20 months ago by ▴ 20
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 5 weeks ago by 43k • written 5.5 years ago by ▴ 110
4
votes
3
replies
318
views
Getting less DE genes when incorporating all samples
RNA-seq differential-expression deseq2
updated 10 weeks ago by ★ 1.8k • written 10 weeks ago by ▴ 10
4
votes
1
reply
568
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
ClusterProfiler RNA-seq GSEA
updated 9 months ago by ★ 1.6k • written 9 months ago by ▴ 100
4
votes
4
replies
652
views
Feedback on mouse brain scRNA-seq quality control
mouse brain singe-cell scRNAseq quality-control
8 months ago by nshenoy ▴ 50
4
votes
4
replies
610
views
Request for a linkage analysis tutorial
linkage
updated 8 months ago by 141k • written 8 months ago by ★ 2.9k
3
votes
2
replies
403
views
t-test by row
R t-test
updated 5 months ago by ★ 1.9k • written 5 months ago by ▴ 20
3
votes
4
replies
633
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR volcano plotting R plot
updated 5 months ago by ★ 1.6k • written 5 months ago by ▴ 260
3
votes
1
reply
520
views
Are there pipelines to analyze the Quality Controls for ATAC-seq and ChIP-seq data?
ChIP-seq ATAC-seq
updated 9 months ago by ★ 2.9k • written 9 months ago by ▴ 180
3
votes
4
replies
1.0k
views
R package DESeq2 in R 3.5.1
R
updated 11 months ago by 43k • written 15 months ago by ▴ 10
3
votes
4
replies
370
views
Single cell analysis with "meta".tsv.gz file
Single-cell
28 days ago by Estevão • 0
3
votes
6
replies
744
views
No genes mapped in clusterprofiler gseGO
R clusterProfiler gseGO GSEA
4 months ago by jon50250 • 0
3
votes
5
replies
536
views
How to assess the quality of the assembly of unmapped reads ?
Pangenome Iterative-assembly
3 months ago by Sony ▴ 10
3
votes
3
replies
2.8k
views
WGCNA Labeled Heatmap
heatmap wgcna
updated 7 months ago by 43k • written 2.6 years ago by ▴ 40
3
votes
6
replies
1.1k
views
6 follow
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics nucleotide_diversity vcf
updated 11 weeks ago by ▴ 10 • written 5 months ago by ▴ 10
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel R statistics
updated 11 months ago by 43k • written 5.1 years ago by ▴ 60
3
votes
4
replies
474
views
Discrepancy between the downloaded clinvar, dbNSFP and website
dbnsfp clinvar
updated 4 months ago by 43k • written 4 months ago by ▴ 40
3
votes
2
replies
1.1k
views
Creating a genotype matrix for BeviMed
snp genome Bayesian
updated 10 months ago by 43k • written 4.3 years ago by ▴ 140
3
votes
5
replies
753
views
STAR error with a loop
STAR RNA transcriptomics
updated 11 months ago by 43k • written 17 months ago by ▴ 50
3
votes
3
replies
341
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio volcano-plot
4 weeks ago by Pumla • 0
3
votes
6
replies
966
views
Embryo transcriptome
database transcriptome SRA
updated 10 months ago by ★ 2.0k • written 11 months ago by • 0
3
votes
6
replies
3.1k
views
Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
gatk variant calling sureselect
updated 9 months ago by • 0 • written 4.2 years ago by ▴ 750
3
votes
5
replies
1.5k
views
Trouble with best practices
samtools WES NGS GATK
updated 11 months ago by 43k • written 6.2 years ago by • 0
3
votes
14
replies
1.2k
views
How to extract specific region from multiple bam files and merge the outputs into single bam?
bam rna-seq
updated 6 months ago by 141k • written 6 months ago by ▴ 770
3
votes
3
replies
867
views
from fasta to gtf format?
gtf DE fasta
updated 3 months ago by ▴ 200 • written 3.0 years ago by ▴ 260
3
votes
1
reply
550
views
chromosome location to gene name and aa change
variant-annotation
11 months ago by Zi • 0
3
votes
6
replies
807
views
Annotating genome based on Sequence
genome annotation
updated 5 months ago by 4.6k • written 6 months ago by ▴ 30
3
votes
1
reply
389
views
FastQC duplicates questions
FastQC RNA-seq
8 months ago by Beth ▴ 10
3
votes
7
replies
489
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
7 weeks ago by Fadlilah ▴ 10
3
votes
7
replies
495
views
How does kallisto handle multi mapped reads?
kallisto
updated 9 weeks ago by ★ 5.9k • written 9 weeks ago by ▴ 150
1,000 results • Page 4 of 20
Recent Votes
Answer: Verify if all the components of a pathway are present in a genomes
Answer: p-value in CIBERSORT
Answer: Can I have multiple active GDC download tokens?
Answer: Can I have multiple active GDC download tokens?
Comment: Can I have multiple active GDC download tokens?
Comment: Programmatically retrieving positions of protein active site residues
Comment: Programmatically retrieving positions of protein active site residues
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Comment: Post-imputation plot by LChart 3.9k
I would pull out the variants with panel_freq ~ 1 - upload_freq and min(panel_freq, upload_freq) < 0.4. I would check if these are G/C or A…
Comment: Telescope issue by eleven11 • 0
Hello the output is A01940:33:GW2208142379th:3:1317:24126:3505 355 chr14 16651125 0 150M = 17034150 122900 GCTAACAGAGTTGAACCTTTCTATTG…
Comment: What does 'bundle_uuid' refer to in this metadata sheet? by GenoMax 141k
Looking at the [code here][1] `bundle_uuid` seems to be related to the submissions to HCA. Samples that ran on multiple lanes seem to have …
Comment: What does it mean single base resolution in sequencing? by LauferVA 4.2k
this is very true and increasingly true as time goes forward. thanks for supplementing this post with your own :-)
Comment: What does 'bundle_uuid' refer to in this metadata sheet? by jeffrey.maurer.informatics • 0
Thank you, but I've already checked out that site to see if I was missing anything and I don't see any answers to my questions there.
Answer: p-value in CIBERSORT by Aspire ▴ 320
You have not explicitly specified the number of permutations (which are used to calculate the p-value). The default value of the permutatio…
Comment: Telescope issue by GenoMax 141k
> CIGAR and query sequence are of different length [W::sam_read1] Parse error at line 9954941 Problem appears to be at that line. Can you …
Comment: KEGG Pathways by Ram 43k
Give us as much detail as you can. What error does it give you?
Comment: What does 'bundle_uuid' refer to in this metadata sheet? by GenoMax 141k
SRA Run Selector shows a better view of the metadata: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA761679&o=acc_s%3Aa
Comment: Adjust pvalue in R with different approach give me all different outcome by Aspire ▴ 320
- `p.adjust()` is supposed to receive a **numeric vector of p-values**, not a matrix. - It makes no sense to "adjust" just one p-value, …
Comment: Downsampling fastq file by marco.barr ▴ 80
I understood where the problem lies. I discussed with my wet lab colleagues (this is part of a bioinformatician's job...) and by showing th…
Comment: Programmatically retrieving positions of protein active site residues by me ▴ 760
This question fits in nicely with the [SIB Swiss Institute of Bioinformatics course on Enzyme information in UniProt][1] [1]: https://w…
Answer: Programmatically retrieving positions of protein active site residues by me ▴ 760
This can be done via SPARQL at the UniProt.org sparql endpoint PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX fald…
Comment: KEGG Pathways by Sudip • 0
No it does not. Do you know of a way that can help me achieve what I want?
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x by GenoMax 141k
UniRef file is 43G compressed so probably will become ~60G when uncompressed. You would likely be looking at at least that much +10-20% GB …
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