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146
votes
34
replies
53k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 9 months ago by 41k • written 10.6 years ago by 6.0k
16
votes
30
replies
53k
views
9 follow
Retrieve The Fasta Nucleic Sequences Of A List Of Ncbi Accession Number Of Proteins
dna sequence retrieval perl bioperl
updated 12.8 years ago by ▴ 290 • written 12.8 years ago by ▴ 90
80
votes
27
replies
53k
views
23 follow
Renaming Entries In A Fasta File
fasta
updated 7.6 years ago by ▴ 50 • written 11.2 years ago by ▴ 130
10
votes
8
replies
53k
views
geom_bar plot with several variables
R ggplot2
updated 4.4 years ago by • 0 • written 4.8 years ago by ▴ 470
76
votes
22
replies
53k
views
17 follow
How To Download All Sra Samples At Once ?
geo sra
updated 8 months ago by 41k • written 9.8 years ago by ★ 1.5k
50
votes
33
replies
53k
views
10 follow
I would like to add gene names to a volcano plot obtained from DEseq2
RNA-Seq DEseq2 R
updated 5.6 years ago by 86k • written 7.4 years ago by ▴ 340
48
votes
19
replies
51k
views
11 follow
How Can I Convert Bam/Sam To Wiggle
wiggle perl samtools
updated 9 months ago by 41k • written 13.2 years ago by ★ 1.4k
91
votes
21
replies
51k
views
13 follow
Should We Remove Duplicated Reads In Rna-Seq ?
rna-seq read
updated 10.0 years ago by ▴ 250 • written 11.1 years ago by ▴ 270
22
votes
4
replies
51k
views
Convert VCFf file to plink ped/map format while filtering the SNPs
vcftools plink ped map
updated 4.8 years ago by • 0 • written 9.2 years ago by ▴ 350
87
votes
25
replies
51k
views
21 follow
How To Split A Multiple Fasta
fasta split
updated 22 months ago by 41k • written 13.3 years ago by ▴ 470
98
votes
12
replies
51k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl entrez gene
updated 2.7 years ago by ▴ 10 • written 11.9 years ago by ▴ 420
10
votes
5
replies
51k
views
Finding number of duplicates in R
R
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by ▴ 70
0
votes
3
replies
51k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 8 months ago by 41k • written 7.5 years ago by ▴ 10
30
votes
20
replies
50k
views
11 follow
List Of All Transcription Factors In Human
transcription ensembl genes
updated 11.2 years ago by 35k • written 11.2 years ago by ▴ 750
37
votes
8
replies
50k
views
11 follow
Adding Read Groups To Bam Files
bam gatk samtools bwa
updated 2.5 years ago by 11k • written 11.5 years ago by 12k
87
votes
37
replies
50k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 21 months ago by 41k • written 10.4 years ago by ▴ 110
36
votes
4
replies
50k
views
TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?
z-scores TCGA RSEM
updated 2.6 years ago by 41k • written 9.4 years ago by ★ 4.1k
46
votes
15
replies
50k
views
11 follow
How to extract specific chromosome from vcf file
vcf
updated 14 months ago by ▴ 560 • written 7.4 years ago by ★ 2.1k
91
votes
50
replies
50k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq pca
updated 2.0 years ago by ▴ 10 • written 6.1 years ago by ▴ 210
35
votes
5
replies
50k
views
Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about that in an assymmetrical matrix
pheatmap R
updated 10 months ago by 41k • written 6.8 years ago by ▴ 180
47
votes
3
replies
50k
views
Gwas Vs. Qtl Mapping?
gwas mapping
updated 17 months ago by 41k • written 11.5 years ago by ▴ 460
60
votes
15
replies
50k
views
11 follow
Estimate Insert Size In Paired-End/Mate-Pair
next-gen sequencing alignment paired
updated 2.1 years ago by 41k • written 11.9 years ago by ▴ 190
6
votes
7
replies
49k
views
matching and merging data frames of different lengths
R
updated 2.2 years ago by 41k • written 9.5 years ago by ▴ 900
10
votes
4
replies
49k
views
BLAST: Identity % and Similarity %
blast
updated 7.5 years ago by ★ 3.9k • written 7.5 years ago by ▴ 40
2
votes
1
reply
49k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 16 months ago by 3.8k • written 16 months ago by ▴ 20
41
votes
16
replies
49k
views
10 follow
How to split paired end SRA file into 2 correct fastq files
next-gen sra fastq
updated 22 months ago by ▴ 10 • written 7.1 years ago by ▴ 130
24
votes
7
replies
49k
views
What Databases Are Available For Rna-Seq Datasets?
rna-seq database geo
updated 11.5 years ago by 18k • written 11.5 years ago by ▴ 140
66
votes
19
replies
49k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 5 months ago by 41k • written 10.8 years ago by ★ 3.6k
57
votes
15
replies
49k
views
11 follow
Filtering Vcf File
vcftools vcf snp indel
updated 21 months ago by 41k • written 11.3 years ago by ▴ 830
16
votes
8
replies
49k
views
9 follow
Ensembl Ids To Gene Name Conversion
gene ensembl
updated 4.7 years ago by • 0 • written 11.6 years ago by ▴ 30
42
votes
7
replies
48k
views
How to extract sample id using bcftools or vcftools
SNP vcf bcftools vcftools
updated 2.4 years ago by ▴ 260 • written 8.6 years ago by ▴ 530
13
votes
5
replies
48k
views
7 follow
Obtaining The Snp Rs Number With The Chromosomal Position
r snps bioconductor
updated 2.2 years ago by ▴ 180 • written 10.6 years ago by ▴ 420
21
votes
11
replies
48k
views
reading a bed file in R
bed R
updated 2.0 years ago by 41k • written 8.0 years ago by ★ 4.2k
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 10 months ago by 41k • written 10.4 years ago by ★ 3.0k
29
votes
9
replies
48k
views
What Is The Difference Between Sequencing Depth And Coverage
sequencing read coverage
updated 12.7 years ago by 53k • written 12.7 years ago by ▴ 970
45
votes
11
replies
48k
views
7 follow
In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
seurat single-cell
updated 2.1 years ago by ★ 16k • written 4.1 years ago by ▴ 770
23
votes
5
replies
48k
views
Any Method Of Converting Bigwig File Format Into Bed Format?
bigwig bed
updated 4.5 years ago by ▴ 200 • written 10.6 years ago by ▴ 50
4
votes
1
reply
48k
views
In ggplot, assign a variable/category to a specific color?
R ggplot plots colors
updated 7.2 years ago by 20 • written 7.3 years ago by ▴ 100
148
votes
70
replies
48k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 3 months ago by ▴ 260 • written 6.0 years ago by 86k
27
votes
15
replies
48k
views
16 follow
how to unzip the files in batch?
next-gen RNA-Seq SNP alignment
updated 10 months ago by 41k • written 8.6 years ago by ▴ 50
4
votes
1
reply
48k
views
ggmaplot error: Unlabeled data points (too many overlaps). Consider increasing max.overlaps
MAplot r ggplot2 ggmaplot
updated 2.4 years ago by 78k • written 2.9 years ago by ▴ 110
29
votes
10
replies
48k
views
How To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
fastq paired-end illumina
updated 9.7 years ago by ★ 2.2k • written 9.7 years ago by ▴ 330
52
votes
21
replies
48k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 5 months ago by 41k • written 11.7 years ago by ★ 1.5k
125
votes
46
replies
47k
views
21 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 8 months ago by 41k • written 7.8 years ago by ★ 3.2k
54
votes
52
replies
47k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 5 months ago by 41k • written 9.3 years ago by 7.5k
65
votes
22
replies
47k
views
7 follow
extract dendrogram cluster from pheatmap
R
updated 22 months ago by • 0 • written 6.0 years ago by ★ 1.1k
30
votes
10
replies
46k
views
Filtering A Sam File For Quality Scores
sam
updated 11.6 years ago by 11k • written 11.6 years ago by ★ 1.3k
2
votes
5
replies
46k
views
Convert text file to VCF file ?
vcf
updated 5 months ago by 41k • written 8.8 years ago by ▴ 260
39
votes
14
replies
46k
views
7 follow
Extraction Of Header Of Sequences In Fasta File
perl fasta python parsing
updated 19 months ago by 53k • written 11.9 years ago by ▴ 350
34
votes
19
replies
46k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene
updated 4 months ago by 41k • written 10.5 years ago by ▴ 250
113,973 results • Page 4 of 2280
Recent Votes
Comment: Annotation Visualization IGV
Comment: Annotation Visualization IGV
Answer: Execute R command on specific termimal
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
Comment: How do I know how much memory to use when piping to with BBMap suite (OutOfMemor
A: difference between GSEA and Gene Ontology
Answer: Does the Minion demultiplex when basecalling?
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Popular Question to samreen.jasvi • 0
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Recent Replies
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Ram 41k
OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Given files `genes.bed` and `snps.bed`, you could do something like: ``` $ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
Answer: How to add exon annotations to genome annotation by alex.zaccaron ▴ 380
You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
and you got answer that should be validate (green tick), or people asked you questions but got no answers.
Comment: Annotation Visualization IGV by awhale01 • 0
Correct I have asked those questions before.
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…
Comment: Ambient RNA removal method that generates whole (integer) counts by EK • 0
Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)
Comment: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.
Answer: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
It might be because Illumina recommends 26 cycles for Read 1: https://knowledge.illumina.com/instrumentation/general/instrumentation-genera…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
Yes at 5%.
Comment: Resolving over clustered NGS with Q-scores by ATpoint 78k
Has phiX been spiked in to increase nucleotide diversity.
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