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119,737 results • Page 4 of 2395
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95
votes
5
replies
57k
views
Difference between Hard Clip and Soft Clip in Samtools CIGAR string
samtools clipped-reads soft-clip bam hard-clip
updated 3.0 years ago by 44k • written 10.3 years ago by ★ 2.6k
98
votes
12
replies
57k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl entrez gene
updated 3.7 years ago by ▴ 10 • written 12.9 years ago by ▴ 420
95
votes
50
replies
57k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq pca
updated 3.0 years ago by ▴ 20 • written 7.1 years ago by ▴ 220
98
votes
21
replies
57k
views
13 follow
Should We Remove Duplicated Reads In Rna-Seq ?
rna-seq read
updated 11.0 years ago by ▴ 250 • written 12.1 years ago by ▴ 290
45
votes
7
replies
57k
views
How to extract sample id using bcftools or vcftools
SNP vcf bcftools vcftools
updated 3.4 years ago by ▴ 260 • written 9.6 years ago by ▴ 560
72
votes
18
replies
56k
views
13 follow
Extracting Multiple Fasta Sequences At A Time From A File Containing Many Sequences
fasta sequence parsing perl
updated 14.2 years ago by 6.0k • written 14.2 years ago by ▴ 110
12
votes
1
reply
56k
views
Interpreting GSEA enrichment plots/results
RNA-Seq gsea
updated 5.3 years ago by ▴ 70 • written 5.8 years ago by ▴ 250
76
votes
22
replies
56k
views
17 follow
How To Download All Sra Samples At Once ?
geo sra
updated 20 months ago by 44k • written 10.8 years ago by ★ 1.5k
15
votes
5
replies
56k
views
R Help: For Loop Over Range Of Number And Calculate Average Using An If Statement
r
updated 8.9 years ago by 20 • written 10.8 years ago by ▴ 110
147
votes
34
replies
56k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 21 months ago by 44k • written 11.6 years ago by 6.1k
22
votes
4
replies
56k
views
Convert VCFf file to plink ped/map format while filtering the SNPs
vcftools plink ped map
updated 5.8 years ago by • 0 • written 10.2 years ago by ▴ 350
23
votes
11
replies
56k
views
reading a bed file in R
bed R
updated 3.0 years ago by 44k • written 9.0 years ago by ★ 4.3k
42
votes
16
replies
55k
views
10 follow
How to split paired end SRA file into 2 correct fastq files
next-gen sra fastq
updated 2.8 years ago by ▴ 10 • written 8.1 years ago by ▴ 130
12
votes
7
replies
55k
views
Use Python To List Filename With Specific Extensions.
python
updated 13.5 years ago by 28k • written 13.5 years ago by ★ 1.7k
4
votes
1
reply
55k
views
ggmaplot error: Unlabeled data points (too many overlaps). Consider increasing max.overlaps
MAplot r ggplot2 ggmaplot
updated 3.4 years ago by 85k • written 3.9 years ago by ▴ 110
82
votes
27
replies
55k
views
23 follow
Renaming Entries In A Fasta File
fasta
updated 8.6 years ago by ▴ 50 • written 12.2 years ago by ▴ 130
27
votes
15
replies
55k
views
16 follow
how to unzip the files in batch?
next-gen RNA-Seq SNP alignment
updated 22 months ago by 44k • written 9.6 years ago by ▴ 50
16
votes
30
replies
55k
views
9 follow
Retrieve The Fasta Nucleic Sequences Of A List Of Ncbi Accession Number Of Proteins
dna sequence retrieval perl bioperl
updated 13.8 years ago by ▴ 290 • written 13.8 years ago by ▴ 90
0
votes
3
replies
55k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 20 months ago by 44k • written 8.5 years ago by ▴ 10
23
votes
22
replies
55k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink vcf fam gatk vcftools
updated 2.0 years ago by • 0 • written 6.6 years ago by ▴ 270
35
votes
5
replies
55k
views
Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about that in an assymmetrical matrix
pheatmap R
updated 22 months ago by 44k • written 7.8 years ago by ▴ 180
42
votes
26
replies
54k
views
11 follow
How To Interpret A T-Test Output Produced By R
statistics
updated 11.4 years ago by 20 • written 12.4 years ago by ★ 1.8k
152
votes
70
replies
54k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 15 months ago by ▴ 260 • written 7.0 years ago by 88k
28
votes
5
replies
54k
views
Any Method Of Converting Bigwig File Format Into Bed Format?
bigwig bed
updated 5.4 years ago by ▴ 210 • written 11.6 years ago by ▴ 50
10
votes
8
replies
54k
views
geom_bar plot with several variables
R ggplot2
updated 5.4 years ago by • 0 • written 5.8 years ago by ▴ 480
88
votes
37
replies
54k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 2.7 years ago by 44k • written 11.4 years ago by ▴ 110
48
votes
19
replies
54k
views
11 follow
How Can I Convert Bam/Sam To Wiggle
wiggle perl samtools
updated 21 months ago by 44k • written 14.2 years ago by ★ 1.4k
76
votes
15
replies
53k
views
10 follow
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
risk minor major reference alleles
written 6.6 years ago by ▴ 420
126
votes
46
replies
53k
views
21 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 20 months ago by 44k • written 8.8 years ago by ★ 3.2k
87
votes
25
replies
53k
views
21 follow
How To Split A Multiple Fasta
fasta split
updated 2.9 years ago by 44k • written 14.3 years ago by ▴ 470
106
votes
109
replies
53k
views
29 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 6 weeks ago by 4.6k • written 6.3 years ago by 88k
37
votes
8
replies
53k
views
11 follow
Adding Read Groups To Bam Files
bam gatk samtools bwa
updated 3.5 years ago by 12k • written 12.5 years ago by 12k
47
votes
3
replies
53k
views
Gwas Vs. Qtl Mapping?
gwas mapping
updated 2.5 years ago by 44k • written 12.4 years ago by ▴ 470
30
votes
20
replies
53k
views
11 follow
List Of All Transcription Factors In Human
transcription ensembl genes
updated 12.2 years ago by 36k • written 12.2 years ago by ▴ 770
5
votes
7
replies
53k
views
PLINK: merge .bed files
plink
updated 24 months ago by 44k • written 9.4 years ago by ▴ 240
58
votes
52
replies
53k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 17 months ago by 44k • written 10.3 years ago by 7.6k
67
votes
19
replies
52k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 17 months ago by 44k • written 11.8 years ago by ★ 3.6k
70
votes
23
replies
52k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 8 months ago by • 0 • written 7.0 years ago by ★ 1.2k
10
votes
12
replies
52k
views
8 follow
Tools to view fastq file
fastq
updated 17 months ago by 44k • written 8.6 years ago by ▴ 40
24
votes
14
replies
52k
views
7 follow
Gene symbol convert to Entrez ID
Entrez R biomart
updated 6.2 years ago by 12k • written 7.5 years ago by ▴ 190
58
votes
15
replies
52k
views
11 follow
Filtering Vcf File
vcftools vcf snp indel
updated 2.8 years ago by 44k • written 12.3 years ago by ▴ 840
29
votes
10
replies
52k
views
How To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
fastq paired-end illumina
updated 10.7 years ago by ★ 2.2k • written 10.7 years ago by ▴ 350
80
votes
16
replies
52k
views
11 follow
How do you cite a tool that doesn't have a publication?
citation academic style
updated 8.6 years ago by 24k • written 8.8 years ago by ★ 1.1k
13
votes
5
replies
52k
views
7 follow
Obtaining The Snp Rs Number With The Chromosomal Position
r snps bioconductor
updated 3.2 years ago by ▴ 180 • written 11.6 years ago by ▴ 460
36
votes
4
replies
51k
views
TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?
z-scores TCGA RSEM
updated 3.6 years ago by 44k • written 10.4 years ago by ★ 4.1k
10
votes
5
replies
51k
views
Finding number of duplicates in R
R
updated 8.3 years ago by ▴ 280 • written 8.3 years ago by ▴ 80
11
votes
4
replies
51k
views
BLAST: Identity % and Similarity %
blast
updated 8.5 years ago by ★ 4.0k • written 8.5 years ago by ▴ 50
33
votes
8
replies
51k
views
7 follow
Difference Between "Pipeline" And "Workflow" ?
next-gen sequencing
written 12.8 years ago by ★ 1.5k
60
votes
15
replies
51k
views
11 follow
Estimate Insert Size In Paired-End/Mate-Pair
next-gen sequencing alignment paired
updated 3.1 years ago by 44k • written 12.9 years ago by ▴ 190
22
votes
4
replies
51k
views
Convert plink files to VCF: Reference allele file
SNP genome
updated 2.2 years ago by 44k • written 9.3 years ago by ▴ 70
119,737 results • Page 4 of 2395
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Comment: biomart hangs
A: Definition of minor and major allele and connection with risk, effect, wildtype
A: Definition of minor and major allele and connection with risk, effect, wildtype
Answer: Question about miRNA nomenclature
Comment: biomart hangs
Comment: biomart hangs
Comment: Convert ensembl ids to gene names
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Comment: biomart hangs by Mark ★ 1.6k
Agreed with Dave, 500 is server error.
Answer: Paired End Data Merging: Before Or After ? by Mark ★ 1.6k
I would not merge. I think historically it was done to improve read quality and improve denovo assembly or alignment (i.e. that muscle link…
Comment: Best Approach to Identify Human-C. elegans Orthologs? by Dunois ★ 2.8k
You can construct your own database by doing a reciprocal best hit search. Use something like [`MMseqs2's rbh`][1] module with both sets of…
Comment: Best Approach to Identify Human-C. elegans Orthologs? by GenoMax 148k
Have you checked: http://www.greenwaldlab.org/ortholist/
Comment: Convert ensembl ids to gene names by anasjamshed ▴ 140
How can I use it for mouse genome?
Comment: Computational tools for predicting novel substrates for a class of enzymes by yarrowmadrona ▴ 10
@hakimbazol Thankyou for our input. Sorry about the late reply. Was off-line a bit with the Thanksgiving holiday. Looks promising. Have you…
Comment: Convert ensembl ids to gene names by GenoMax 148k
Use https://bioconductor.org/packages/release/bioc/html/biomaRt.html <!-- this is it -->
Comment: Convert ensembl ids to gene names by anasjamshed ▴ 140
I want to this by R as I am doing gene expression analysis and have to made volcano plots
Comment: biomart hangs by Dave Carlson ★ 2.0k
I have been having problems connecting to various Ensembl sites for the past week or two. I think maybe they're experiencing some issues.
Answer: abra2 error java.lang.NumberFormatException by phage1 • 0
inputs need to be sorted and indexed. can you confirm you are doing this? samtools sort input.bam -o sorted.bam samtools index sor…
Answer: Convert ensembl ids to gene names by GenoMax 148k
> Convert ensembl ids to gene names This is a frequently asked question on biostars. I will include one example of a prior thread but you …
Answer: gene annotation of an eukaryotic organism by francis ▴ 260
What organism? What size? Please define by what you want to do when you say "annotation of a genome" or "gene annotation". Have you r…
Answer: Counts after using feature counts is low by swbarnes2 14k
No one can troubleshoot from just this. Have you looked at the obvious source of error; did you get the gtf and the genome from the same s…
Answer: contrast matrix design for a continuous variable at multiple groups by Asaf 10k
The element V1 will give you the overall effect of V1. V1:Sex interaction will answer the question how V1 is different between males and fe…
Comment: RNA-seq to look at the Effect of Viral Infection by swbarnes2 14k
DESEq is going to find the gene whose expression is in the "middle" (using the geometric mean of each gene across all samples) and assume t…
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