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11,716 results • Page
2 of 235
Sort: Votes
Rank
Views
Votes
Replies
82
votes
27
replies
21k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq
atac-seq
normalization
updated 7 weeks ago by
sgv
• 0 • written 4.4 years ago by
Flo
▴ 250
81
votes
21
replies
43k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 8 months ago by
Joel Wallenius
▴ 210 • written 10.3 years ago by
pristanna
▴ 750
81
votes
26
replies
13k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 7 months ago by
Ram
44k • written 14.2 years ago by
User 59
13k
80
votes
21
replies
37k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 6 months ago by
kathryn.jacksonjones
• 0 • written 10.1 years ago by
M K
▴ 660
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 6 months ago by
Ram
44k • written 14.1 years ago by
Giovanni M Dall'Olio
28k
79
votes
86
replies
32k
views
20 follow
Tool:
Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify
storage
bbmap
pigz
compression
updated 11 months ago by
Ram
44k • written 7.5 years ago by
Brian Bushnell
20k
78
votes
38
replies
33k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 12 weeks ago by
nickp60
▴ 60 • written 7.9 years ago by
andrew.j.skelton73
6.6k
77
votes
26
replies
122k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 6 months ago by
cschu181
★ 2.8k • written 9.1 years ago by
Chenglin
▴ 260
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
4 weeks ago by
Kevin Blighe
88k
76
votes
14
replies
13k
views
10 follow
Tool:
karyoploteR: uncircle your genomes
karyoploteR
Rdataviz
NGS
updated 11 months ago by
Ram
44k • written 7.0 years ago by
bernatgel
★ 3.4k
75
votes
19
replies
3.6k
views
11 follow
Blog:
A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 12 weeks ago by
LauferVA
4.2k • written 8 months ago by
Kenny
▴ 30
75
votes
15
replies
36k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing
duplicates
updated 6 months ago by
Ram
44k • written 14.1 years ago by
Pierre Lindenbaum
162k
74
votes
16
replies
4.9k
views
10 follow
Tools & Techniques Bioinformatician Have To Master?
subjective
updated 11 months ago by
Ram
44k • written 13.2 years ago by
Thaman
★ 3.3k
73
votes
14
replies
4.3k
views
12 follow
Forum:
Things you wish you knew when entering the bioinformatics field
pitfalls
advice
updated 11 months ago by
Ram
44k • written 3.7 years ago by
jared.andrews07
★ 17k
73
votes
27
replies
28k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 months ago by
snardeli
• 0 • written 10.3 years ago by
Istvan Albert
100k
72
votes
71
replies
32k
views
17 follow
Tool:
EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot
bioconductor
ggplot2
ggrepel
updated 11 months ago by
Ram
44k • written 5.7 years ago by
Kevin Blighe
88k
71
votes
15
replies
49k
views
10 follow
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
risk
minor
major
reference
alleles
written 6.1 years ago by
m98
▴ 420
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 10 weeks ago by
jkbonfield
★ 1.2k • written 5.2 years ago by
finswimmer
16k
69
votes
25
replies
7.1k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 6 months ago by
Ram
44k • written 14.2 years ago by
Dave Gerrard
▴ 190
68
votes
23
replies
50k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 10 weeks ago by
Getnet Tesfaw
• 0 • written 6.5 years ago by
1769mkc
★ 1.2k
68
votes
18
replies
132k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing
samtools
updated 4 months ago by
Pierre Lindenbaum
162k • written 9.6 years ago by
Kizuna
▴ 870
68
votes
25
replies
16k
views
12 follow
Tool:
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq
SRA
updated 7 months ago by
GenoMax
142k • written 5.2 years ago by
Phil Ewels
★ 1.4k
66
votes
23
replies
11k
views
9 follow
Using Hdf5 To Store Bio-Data
hdf5
storage
database
updated 7 months ago by
Ram
44k • written 14.3 years ago by
Pierre Lindenbaum
162k
66
votes
19
replies
51k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 11 months ago by
Ram
44k • written 11.3 years ago by
14134125465346445
★ 3.6k
65
votes
10
replies
3.5k
views
6 follow
Incentive For Learning Emboss
emboss
updated 11 months ago by
Ram
44k • written 13.1 years ago by
Eric Normandeau
11k
65
votes
24
replies
17k
views
14 follow
Mapping Snps To Pathways
snp
genotyping
pathway
gene
enrichment
updated 7 months ago by
Ram
44k • written 14.2 years ago by
Pierre Lindenbaum
162k
64
votes
25
replies
57k
views
22 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 8 hours ago by
GenoMax
142k • written 11.4 years ago by
rehma.ar
▴ 290
61
votes
23
replies
57k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam
mapping
updated 6 months ago by
Lluís R.
★ 1.2k • written 11.3 years ago by
Jordan
★ 1.3k
61
votes
51
replies
22k
views
9 follow
Tool:
Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files
sff
sequence
fastq
next-gen
updated 11 months ago by
Ram
44k • written 10.1 years ago by
BioApps
▴ 790
61
votes
14
replies
11k
views
11 follow
Recommend Easy To Use Microarray Clustering Software
microarray
clustering
updated 7 months ago by
Ram
44k • written 14.7 years ago by
Istvan Albert
100k
60
votes
25
replies
6.0k
views
8 follow
Forum:
Am I crazy, or are most published RNA-seq studies vastly underpowered?
sample-size
statistical-power
RNA-Seq
updated 11 months ago by
Ram
44k • written 3.8 years ago by
telroyjatter
▴ 230
60
votes
21
replies
3.9k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome
assembly
updated 8 months ago by
Michael
54k • written 9 months ago by
sqshigg
▴ 60
60
votes
25
replies
22k
views
17 follow
Which Operating System Do You Prefer For Bioinformatics?
general
subjective
updated 7 months ago by
Ram
44k • written 14.3 years ago by
Giovanni M Dall'Olio
28k
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 6 months ago by
Ram
44k • written 14.1 years ago by
Khader Shameer
18k
58
votes
8
replies
8.5k
views
8 follow
What is the best way to combine machine learning algorithms for feature selection such as Variable importance in Random Forest with differential expr…
RNA-Seq
rna-seq
updated 7 months ago by
Di Wu
• 0 • written 6.2 years ago by
elmahy2005
▴ 150
57
votes
22
replies
29k
views
7 follow
Batch correction in DESeq2
Combat
DESeq2
Batch-Effect
updated 7 weeks ago by
Ram
44k • written 4.6 years ago by
Arindam Ghosh
▴ 510
57
votes
35
replies
15k
views
9 follow
How to get sample names and genotype for SNP in multi-sample VCF file
SNP
genotype
GATK
updated 7 months ago by
Kevin Blighe
88k • written 6.3 years ago by
hellbio
▴ 520
56
votes
52
replies
50k
views
12 follow
Tool:
Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF
Gene-Clustering
updated 11 months ago by
Ram
44k • written 9.8 years ago by
EagleEye
7.5k
56
votes
23
replies
5.2k
views
10 follow
Tool:
ASCIIGenome: Text Only Genome Viewer!
terminal
genome-browser
java
ASCIIGenome
updated 11 months ago by
Ram
44k • written 7.9 years ago by
dariober
14k
56
votes
12
replies
12k
views
9 follow
What Are The Public Sql Servers For Bioinformatics ?
online-server
sql
updated 6 months ago by
Ram
44k • written 14.2 years ago by
Pierre Lindenbaum
162k
54
votes
10
replies
22k
views
10 follow
Finding Common Motifs In Sequences
motif
updated 7 months ago by
Ram
44k • written 14.7 years ago by
Fabio
▴ 130
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 5 weeks ago by
kjngo
• 0 • written 12.1 years ago by
Gabriel R.
★ 2.9k
54
votes
13
replies
10k
views
6 follow
Tool:
Bedtools: Analyzing Genomic Features
bedtools
updated 11 months ago by
Ram
44k • written 12.1 years ago by
Istvan Albert
100k
54
votes
7
replies
4.0k
views
6 follow
Tool:
Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinformatics
genome-viewer
updated 11 months ago by
Ram
44k • written 11.0 years ago by
chbelhumeur2000
▴ 40
54
votes
15
replies
30k
views
10 follow
Where To Download Pam50 Gene Set?
cancer
annotation
classification
updated 10 months ago by
DareDevil
★ 4.3k • written 10.8 years ago by
user
▴ 940
53
votes
13
replies
7.9k
views
9 follow
Has Enhancer And Transcription Factor Binding Site Prediction Already Been Made Redundant?
transcription-factor-binding-site
updated 7 months ago by
Ram
44k • written 14.2 years ago by
Allpowerde
★ 1.3k
52
votes
8
replies
20k
views
6 follow
Fast Interval Intersection Methodologies
genomics
updated 7 months ago by
Ram
44k • written 14.2 years ago by
Biostar User
★ 1.0k
52
votes
8
replies
60k
views
7 follow
Subsampling Bam File With Samtools
bam
samtools
updated 4 months ago by
giulia.trauzzi
▴ 10 • written 10.9 years ago by
madbessoul
▴ 250
52
votes
14
replies
41k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing
fastq
updated 6 months ago by
Pierre Lindenbaum
162k • written 14.1 years ago by
Zach Stednick
▴ 660
52
votes
21
replies
49k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 11 months ago by
Ram
44k • written 12.2 years ago by
Geparada
★ 1.5k
11,716 results • Page
2 of 235
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Answer: Help me with simple data for RNA seq
A: Most Popular and fancy SNP analysis tools Comparison: Plink, SNPassoc, SNPRelate
Most Popular and fancy SNP analysis tools Comparison: Plink, SNPassoc, SNPRelate
GWAS analysis tool
Answer: Cut&Run and heatmap
Comment: Functional enrichment analysis for unique gene IDs
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
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Recent Replies
Answer: Help with proteomics downstream analysis
by
Nat.Nataren
▴ 10
I would be contacting the company as a start, and getting access to your raw data.
Comment: txt file to bigwig
by
ATpoint
82k
Please stop asking questions in existing threads. Delete these two comments and open a new question with all the necessary details to under…
Comment: Venter Genome Vcf
by
Jeremy Leipzig
22k
there are some violations in this VCF: - Invalid count number, with fixed count the number should be 1 or higher: key=INFO name=TSA type=St…
Comment: Cut&Run and heatmap
by
sogand
• 0
Hi all, I am new to cut&run or any peak-related analysis and appreciate any guidance on my issue here: I have analyzed peakcalling .txt …
Comment: Functional enrichment analysis for unique gene IDs
by
Pegasus
▴ 100
Since the locus-tags are unclassified, I used the CDS instead of the locus-tags to retrive their ensembl IDs using ensembl bacteria website…
Comment: samtools mpileup error - 1 samples in 1 input files
by
Damla
• 0
Could you find a solution to your problem?
Comment: txt file to bigwig
by
sogand
• 0
Hi all, I am new to these kind of analysis and appreciate any guidance on my issue here: I have analyzed peakcalling .txt files that are r…
Answer: Help me with Heatmap
by
MolGeek
▴ 50
Hello! So, what is the correct design ? You will have to ask yourself, what do you want to compare? WT vs mut? If so it will be strain. 2…
Answer: Help me with simple data for RNA seq
by
swbarnes2
14k
1) you have to say what question you are actually asking. There are few different designs that would address different questions. 2) work…
Comment: identify the coordinate for coding and non_coding region.
by
Ghada
• 0
mmmm I am not sure. This is how I generate my consnsus sequence # Get consensus fastq file samtools mpileup -uf KT992094.1.fasta…
Comment: identify the coordinate for coding and non_coding region.
by
GenoMax
142k
Why do you have those N's at the beginning of the sequence? If the remainder of the sequence matches 100% then the initial N's may be wrong…
Answer: Salmon vs Kallisto vs RSEM
by
Rob
6.6k
It's nice that you've gone ahead and done some analysis of these results and their differences on your data yourself. These more general qu…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Mike Smith
★ 2.0k
In this location there is an "entrez" file which maps ensembl IDs to Entrez. It's probably as definitive as you're going to find: https://…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Tried it just recently with almost the same results. 456 out of 496 IDs for protein-coding genes returned as "NA" even though I can see NCB…
Answer: Download All The Bacterial Genomes From Ncbi
by
2284046470
• 0
wget https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt awk -F '\t' '{if($12=="Complete Genome" && $11=…
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