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1,000 results • Page 3 of 20
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31
votes
11
replies
41k
views
9 follow
How To Sort Sam File
samtools sam
updated 10 weeks ago by 38k • written 9.1 years ago by ★ 1.1k
44
votes
15
replies
41k
views
11 follow
How to extract specific chromosome from vcf file
vcf
updated 5 months ago by ▴ 510 • written 6.7 years ago by ★ 2.0k
27
votes
15
replies
41k
views
16 follow
how to unzip the files in batch?
next-gen RNA-Seq SNP alignment
updated 6 weeks ago by 38k • written 7.9 years ago by ▴ 50
51
votes
19
replies
41k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 28 days ago by 38k • written 10.9 years ago by 11k
79
votes
6
replies
41k
views
6 follow
Read Group In Sam/Bam Files: What Do They Exactly Describe?
bam samtools next-gen
updated 12 months ago by 38k • written 10.9 years ago by 4.3k
26
votes
9
replies
40k
views
How Logfc Value Is Calculated In Edger?
edger r RNA-seq
updated 20 days ago by 38k • written 9.5 years ago by ▴ 240
131
votes
27
replies
40k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 11 months ago by 38k • written 10.9 years ago by 33k
39
votes
17
replies
40k
views
13 follow
Extract Cds Fastas From A Gff Annotation + Reference Sequence
gff CDS
updated 6 weeks ago by 38k • written 10.8 years ago by ▴ 700
116
votes
66
replies
40k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 7 days ago by 38k • written 4.7 years ago by 70k
109
votes
56
replies
40k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 6 months ago by 38k • written 10.8 years ago by ▴ 380
46
votes
9
replies
40k
views
9 follow
How To Convert Centimorgan To Base Pair
genetics distance
updated 5 months ago by 38k • written 11.2 years ago by ▴ 90
33
votes
11
replies
39k
views
8 follow
Where Can I Download Some Bam Files?
bam RNA-seq
updated 28 days ago by 38k • written 10.8 years ago by ▴ 160
60
votes
52
replies
39k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 6 days ago by 38k • written 6.5 years ago by ★ 3.3k
20
votes
4
replies
39k
views
Convert plink files to VCF: Reference allele file
SNP genome
updated 5 months ago by 38k • written 7.6 years ago by ▴ 70
5
votes
7
replies
38k
views
PLINK: merge .bed files
plink
updated 3 months ago by 38k • written 7.7 years ago by ▴ 210
14
votes
6
replies
38k
views
7 follow
How To Convert A Fasta Or Alignment File To Nexus (.Nex) File That Is To Be Used In The Beast Program
updated 6 months ago by ▴ 210 • written 9.6 years ago by ▴ 20
105
votes
26
replies
38k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 5 months ago by 38k • written 10.2 years ago by ▴ 810
62
votes
24
replies
38k
views
12 follow
How to extract unique mapped results from Bowtie2 bam results?
alignment
updated 11 weeks ago by 38k • written 8.8 years ago by ▴ 170
206
votes
58
replies
38k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 24 days ago by 38k • written 9.8 years ago by 9.5k
34
votes
8
replies
38k
views
9 follow
Difference Between "Mate Pair" And "Pair-End"
paired-end ngs library
updated 3 months ago by ★ 2.9k • written 9.7 years ago by ▴ 130
28
votes
14
replies
37k
views
8 follow
Running and Analyzing fastqc on multiple fastq files
next-gen RNA-Seq genome
updated 6 weeks ago by 38k • written 7.9 years ago by ▴ 220
23
votes
22
replies
37k
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 3 months ago by • 0 • written 4.9 years ago by ▴ 250
14
votes
2
replies
37k
views
what is difference between sequence adapter and PCR primer?
adapter pcr
updated 10 weeks ago by 38k • written 7.8 years ago by ▴ 110
20
votes
12
replies
37k
views
7 follow
Forum: When To Use Sed Awk Over Perl Or Python
perl python awk
updated 19 days ago by 38k • written 9.2 years ago by 9.5k
94
votes
31
replies
37k
views
17 follow
What Is The Quickest Algorithm For Range Overlap?
python alignment next-gen sequencing database
updated 11 months ago by 38k • written 12.6 years ago by ▴ 280
19
votes
5
replies
37k
views
linkage disequilibrium: difference between D' and r-squared
ld r-squared
updated 10 months ago by 38k • written 8.1 years ago by ▴ 60
26
votes
14
replies
36k
views
8 follow
How To Retrieve Genbank Records With Range Of Accession Numbers
genbank
updated 11 months ago by ★ 2.9k • written 12.4 years ago by 4.1k
44
votes
8
replies
36k
views
6 follow
Tool: Tools to merge overlapping paired-end reads
overlapping Assembly ngs fastq Tool
updated 5 months ago by • 0 • written 6.3 years ago by ★ 1.2k
115
votes
35
replies
36k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow Forum
updated 10 days ago by ▴ 30 • written 5.8 years ago by ▴ 760
58
votes
25
replies
36k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 3 days ago by 38k • written 6.6 years ago by ★ 9.3k
25
votes
12
replies
36k
views
7 follow
Log2 Ratio or Log2 Fold Change - terminology confusion and which one should I use?
genome
updated 8 months ago by ▴ 30 • written 6.4 years ago by ▴ 150
48
votes
17
replies
35k
views
17 follow
How To Get Number Of Reads In Bam File Efficiently In Python?
python samtools next-gen sequencing
updated 4 months ago by 38k • written 12.7 years ago by ▴ 830
27
votes
13
replies
35k
views
10 follow
Survival Analysis Using Tcga Data
tcga bioinformatician
updated 5 weeks ago by 38k • written 9.0 years ago by ▴ 500
45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 4 weeks ago by 38k • written 11.0 years ago by ▴ 540
116
votes
31
replies
35k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 9 months ago by 38k • written 9.6 years ago by 11k
41
votes
17
replies
35k
views
15 follow
Forum: List Of Genome Sequencing Centers/Institutes
genomics institutes
updated 25 days ago by 38k • written 10.1 years ago by 19k
10
votes
4
replies
35k
views
merge two data frame with different length
R
updated 9 months ago by 38k • written 8.0 years ago by ▴ 70
46
votes
20
replies
35k
views
13 follow
Counting Number Of Bases In A Fastq File
fastq ngs
updated 8 months ago by • 0 • written 9.6 years ago by ▴ 180
16
votes
7
replies
34k
views
6 follow
hg38 annotation file (gtf) UCSC format
RNA-Seq alignment
updated 7 months ago by 38k • written 7.1 years ago by ▴ 160
21
votes
18
replies
34k
views
10 follow
Combining Data Of Multiple Vcfs Into One.
vcf variant-calling
written 9.8 years ago by ▴ 410
59
votes
36
replies
34k
views
27 follow
Pca From Vcf Files
pca genome vcf
updated 7 months ago by ▴ 40 • written 10.9 years ago by ▴ 820
11
votes
4
replies
34k
views
Forum: BWA command guide
BWA
updated 5 weeks ago by 38k • written 5.1 years ago by ★ 1.1k
92
votes
105
replies
34k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 7 days ago by 38k • written 4.6 years ago by 84k
60
votes
12
replies
34k
views
10 follow
Get chromosome sizes from fasta file
genome ucsc
updated 4 months ago by • 0 • written 7.2 years ago by ▴ 690
33
votes
12
replies
33k
views
7 follow
How Can I Count Snps In My Vcf Files?
vcf snp awk
updated 6 months ago by 38k • written 10.7 years ago by ▴ 250
12
votes
10
replies
33k
views
9 follow
How To Convert Vcf File To Plink Ped Format?
vcftools
updated 5 months ago by 38k • written 12.1 years ago by ▴ 40
13
votes
3
replies
33k
views
Drawing venn diagram in R
ChIP-Seq venn diagram Forum
updated 8 months ago by 38k • written 7.9 years ago by ▴ 450
52
votes
11
replies
33k
views
8 follow
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
RNA-Seq
updated 7 weeks ago by 38k • written 8.7 years ago by ▴ 210
18
votes
18
replies
33k
views
8 follow
BLAST, setting maximum number of hits
BLAST tblastx parallel
updated 10 months ago by 38k • written 8.1 years ago by ▴ 480
6
votes
6
replies
32k
views
Can the code of a R package be changed? How?
R
updated 11 weeks ago by 38k • written 7.8 years ago by ★ 5.0k
1,000 results • Page 3 of 20
Recent Votes
Answer: How to implement this two-stage one-to-many workflow using WDL?
Answer: How to implement this two-stage one-to-many workflow using WDL?
Answer: How to implement this two-stage one-to-many workflow using WDL?
Creating workflows with snakemake and conda
Is There A Way To Run Fastqc On All The Fastq Files In The Different Directories With Just One Command?
Is There A Way To Run Fastqc On All The Fastq Files In The Different Directories With Just One Command?
Comment: samtools idxstats not removing ChrM
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Recent Replies
Comment: gene filtering for agilent microarray using Limma by Di Wu • 0
Dear Prof. Kevin Blighe, many thanks for your quick reply. About the `correlation` value, I used the following code for getting the value. …
Comment: GATK GenotypeGVCFs explain by Pierre Lindenbaum 153k
https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists
Comment: GATK GenotypeGVCFs explain by Sarah ▴ 30
thank you
Comment: GATK GenotypeGVCFs explain by raphael.B ▴ 270
It limits the operation to some genomic regions given as parameter
Comment: GATK GenotypeGVCFs explain by Sarah ▴ 30
what does the option L
Comment: GATK GenotypeGVCFs explain by Pierre Lindenbaum 153k
GenotypeGVCFs takes a set of GVCF files called with HaplotyperCaler and output a VCF file.
Answer: TCGA Methylation Data and Gene Mapping by Basti ★ 1.4k
CpGs may be annotated to more than >1 gene simply because gene regions overlap on the genome. If you want to associate each gene to a me…
Comment: Circos plot by Fabio Marroni ★ 3.0k
Please give a look to [this post][1] for increasing the probability to get an answer. If I may add some needed info: 1. What exactly do y…
Comment: Trying to install Roary with Conda results in error message by tobiwan ▴ 10
Wow, thank you so much for your explanation! My conda channel is indeed set to strict priority. Should packages with different dependencie…
Comment: FeatureCounts >edgeR > GO by Basti ★ 1.4k
You can use BioMart to convert your "gene-IDs" to gene symbols, but you need to specify from which database your gene identifiers come from
Comment: How to create GO Bar Plot using data obtained from DAVID Functional Enrichment A by Basti ★ 1.4k
If you search "DAVID dotplot" on this forum, you have many answers to your question. Note that you can also perform DAVID Functional Enrich…
Answer: How to implement this two-stage one-to-many workflow using WDL? by Pierre Lindenbaum 153k
nottested, something like: ``` version 1.0 workflow BIOSTAR { call FIRST { } scatter (F in FIRST.each_F)…
Answer: Databases to check variant pathogenicity by AtenaLia ▴ 20
You can try https://genebe.net , it is similar to Varsome though...
Answer: ACMG assignment tools by AtenaLia ▴ 20
Hi, free ACMG implementation without restrictions can be found at https://genebe.net . AFAIK there is also a free API coming.
Comment: Bad quality fastq files for analysis by Gene_MMP8 ▴ 220
I don't have the data available. I want to identify such datasets. The overall aim is to determine what factors influence fastq data qualit…
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