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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
115
votes
52
replies
85k
views
21 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 4 days ago by
Ram
37k • written 8.6 years ago by
kay
▴ 320
166
votes
41
replies
83k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence
fasta
updated 5 days ago by
Onur
• 0 • written 11.6 years ago by
Palu
▴ 240
70
votes
20
replies
79k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl
identifiers
mapping
updated 29 days ago by
Ram
37k • written 12.2 years ago by
Unode
▴ 180
33
votes
17
replies
68k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray
heatmap
updated 16 days ago by
Ram
37k • written 11.7 years ago by
Fahmida
▴ 80
76
votes
19
replies
68k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools
bcftools
htslib
Tutorial
updated 13 days ago by
jcurry01
• 0 • written 4.5 years ago by
otwtgin2010
▴ 520
194
votes
44
replies
67k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 26 days ago by
Ram
37k • written 10.4 years ago by
Obi Griffith
20k
1.2k
votes
205
replies
47k
views
107 follow
Forum:
What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 18 days ago by
jena
▴ 240 • written 11.8 years ago by
Jeremy Leipzig
21k
9
votes
7
replies
42k
views
R programming: compare columns to column and get the mismatch
R
updated 3 days ago by
Ram
37k • written 7.8 years ago by
MAPK
★ 2.0k
31
votes
11
replies
41k
views
9 follow
How To Sort Sam File
samtools
sam
updated 26 days ago by
Ram
37k • written 9.0 years ago by
Chen Sun
★ 1.1k
27
votes
15
replies
40k
views
16 follow
how to unzip the files in batch?
next-gen
RNA-Seq
SNP
alignment
updated 3 days ago by
Ram
37k • written 7.7 years ago by
flavobacteria
▴ 50
205
votes
58
replies
38k
views
31 follow
Forum:
Will Python Take The Place Of R?
biopython
statistics
r
python
Forum
updated 5 days ago by
Ram
37k • written 9.7 years ago by
Medhat
9.5k
28
votes
14
replies
37k
views
8 follow
Running and Analyzing fastqc on multiple fastq files
next-gen
RNA-Seq
genome
updated 1 day ago by
Ram
37k • written 7.7 years ago by
ravi.uhdnis
▴ 220
50
votes
11
replies
33k
views
8 follow
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
RNA-Seq
updated 11 days ago by
Ram
37k • written 8.6 years ago by
thisismytest3023
▴ 200
92
votes
105
replies
32k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial
1000
genomes
PCA
PLINK
updated 4 days ago by
s.w.vanderlaan
▴ 40 • written 4.4 years ago by
Kevin Blighe
84k
115
votes
25
replies
32k
views
20 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq
Kallisto
RNASeq
Salmon
DESeq2
updated 16 days ago by
Ram
37k • written 7.7 years ago by
mhockin
▴ 600
40
votes
10
replies
32k
views
7 follow
Can'T Locate Vcf.Pm Vcftools
vcftools
vcf
updated 1 day ago by
Ram
37k • written 11.2 years ago by
Deniz
▴ 210
94
votes
25
replies
31k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
fastq
trimming
qc
tutorial
Tutorial
updated 5 days ago by
Ram
37k • written 10.4 years ago by
Istvan Albert
96k
71
votes
17
replies
30k
views
14 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 18 days ago by
Ming Tang
★ 2.9k • written 8.8 years ago by
M K
▴ 590
117
votes
59
replies
29k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware
next-gen
updated 1 day ago by
Ram
37k • written 7.7 years ago by
Angelo Victoria
▴ 30
42
votes
21
replies
28k
views
16 follow
Multi-Sample Vcf To Phylogenetic Tree.
vcf
updated 16 days ago by
Ram
37k • written 9.3 years ago by
William
★ 5.1k
25
votes
35
replies
28k
views
16 follow
Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
mpileup
updated 4 days ago by
Jan Röslein
▴ 10 • written 8.9 years ago by
komal.rathi
★ 4.0k
99
votes
36
replies
27k
views
32 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 12 days ago by
Jeremy Leipzig
21k • written 9.2 years ago by
14134125465346445
★ 3.6k
19
votes
15
replies
25k
views
6 follow
tophat-cufflinks command pipeline
cufflinks
tophat
updated 16 days ago by
Ram
37k • written 8.1 years ago by
biolab
★ 1.4k
25
votes
7
replies
25k
views
Is Paired End analysis possible with FASTQC?
dna-seq
QC
paired-end
fastqc
updated 25 days ago by
Ram
37k • written 6.7 years ago by
chefarov
▴ 160
296
votes
121
replies
24k
views
29 follow
Mean Length Of Fasta Sequences
code
fasta
sequence
codegolf
updated 4 days ago by
jena
▴ 240 • written 12.6 years ago by
Eric Normandeau
11k
55
votes
23
replies
24k
views
11 follow
Remove duplicates in fasta file based on ID
fasta
sort
sed
updated 18 days ago by
Ram
37k • written 7.7 years ago by
oliver.bayfield
▴ 210
13
votes
8
replies
24k
views
How to generate a fasta file from a python dictionary or lists?
sequence
fasta
list
dictionary
python
updated 4 days ago by
Ram
37k • written 7.7 years ago by
grayapply2009
▴ 240
68
votes
26
replies
24k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq
tutorial
Tutorial
updated 11 days ago by
Ram
37k • written 9.0 years ago by
Istvan Albert
96k
66
votes
6
replies
23k
views
8 follow
What Is A "Spot" In Sra Format
sra
fastq
format
updated 11 days ago by
Ram
37k • written 11.4 years ago by
Daniel Standage
4.1k
13
votes
11
replies
22k
views
9 follow
Where Can I Get The Asperasoft Command Line Client Ascp
sra
aspera
updated 19 days ago by
GenoMax
125k • written 10.4 years ago by
Jeremy Leipzig
21k
30
votes
13
replies
22k
views
7 follow
Difference between tSNE and PCA analysis
next-gen
rna-seq
updated 11 days ago by
Yogi
• 0 • written 5.0 years ago by
Qingyang Xiao
▴ 160
38
votes
11
replies
20k
views
11 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq
DESeq2
geneontology
GSEA
updated 4 days ago by
Oliver
• 0 • written 5.3 years ago by
Sreeraj Thamban
▴ 280
87
votes
16
replies
19k
views
15 follow
Are we tricking ourselves with batch effect correction?
combat
batch-effect
sva
updated 6 days ago by
madbadradscientist
▴ 20 • written 7.7 years ago by
Christian
★ 3.0k
11
votes
8
replies
19k
views
7 follow
Convert Ensembl Transcript Ids Ensmust To Gene Symbol Using Mygene Module In Python
python
ensembl
convert
gene
updated 5 days ago by
Francesco
• 0 • written 9.0 years ago by
hicsuntdrac0nis
▴ 240
13
votes
14
replies
18k
views
7 follow
Get Fasta File With Protein Sequences Given Entrez Gene Ids
entrez
eutils
fasta
updated 16 days ago by
Ram
37k • written 10.4 years ago by
Stephen
2.8k
14
votes
9
replies
18k
views
7 follow
Error: unable to open file or unable to determine types for file bed file
sequencing
bed
bedtools
updated 7 days ago by
Neel
▴ 10 • written 8.0 years ago by
sebastianzeki0
▴ 190
38
votes
63
replies
17k
views
24 follow
Recommendations For Heterozygous Genome Assembly Software
assembly
miseq
illumina
genome
updated 26 days ago by
Ram
37k • written 10.0 years ago by
Leszek
4.2k
15
votes
12
replies
16k
views
6 follow
difference between GSEA and Gene Ontology
gene ontology
GSEA
RNA-Seq
updated 23 days ago by
Neel
▴ 10 • written 6.6 years ago by
GHanumanth404
▴ 20
39
votes
11
replies
15k
views
11 follow
Best Database Of Transcription Factor Binding Sites
transcription
binding
database
updated 9 days ago by
nta
• 0 • written 11.9 years ago by
Dataminer
★ 2.7k
27
votes
50
replies
15k
views
7 follow
Extract fasta sequences from a large file using a list of names
16s
fasta
extract
updated 1 day ago by
Ram
37k • written 7.8 years ago by
fhsantanna
▴ 600
4
votes
8
replies
14k
views
[WGCNA] Error in goodSamplesGenes function
RNA-Seq
wgcna
R
updated 3 days ago by
Ram
37k • written 8.0 years ago by
gustavoborin01
▴ 90
2
votes
1
reply
14k
views
How to use Combat in R??
R
software-error
Combat
updated 12 days ago by
Ram
37k • written 7.7 years ago by
madkitty
▴ 660
29
votes
3
replies
14k
views
In Cigar String, What Is The Difference Between 'N' And 'D' ?
cigar
bam
sam
updated 11 days ago by
Ram
37k • written 8.9 years ago by
Chen Sun
★ 1.1k
59
votes
95
replies
14k
views
8 follow
How to extract the list of genes from TCGA CNV data
TCGA
CNV
genes
updated 1 day ago by
Di
▴ 10 • written 4.8 years ago by
Chaimaa
▴ 260
16
votes
26
replies
14k
views
16 follow
bedtools coverage gives error received illegal bin number, but that number isn't in my data!
ChIP-Seq
bedtools
updated 16 days ago by
Ram
37k • written 6.0 years ago by
tara.alpert
▴ 30
2
votes
3
replies
13k
views
Bootstrap values on a phylogenetic tree (RAxML).
PAxML
bootstrap
phylogenetic-tree
updated 2 days ago by
Ram
37k • written 7.7 years ago by
vasilislenis
▴ 150
13
votes
12
replies
13k
views
6 follow
Normalization Of Rna Sequencing Counts (By Ercc / Gene Length)
rnaseq
normalization
deseq
edger
updated 12 days ago by
Ram
37k • written 9.0 years ago by
Sam
★ 4.6k
10
votes
8
replies
13k
views
6 follow
Is the heterozygosity flag (--het) in vcftools calculate observed and expected heterozygosity?
vcftools
vcf
updated 1 day ago by
dr.fakharunnisa
• 0 • written 5.5 years ago by
ahmedaljumiliy
▴ 40
47
votes
19
replies
12k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 25 days ago by
Ram
37k • written 9.9 years ago by
Istvan Albert
96k
19
votes
11
replies
12k
views
How to work with Level 3 data (RPKM values) from TCGA database
RNA-Seq
TCGA
updated 26 days ago by
Ram
37k • written 7.7 years ago by
pbio
▴ 150
1,000 results • Page
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Recent Replies
Comment: PLINK2 selecting variants based on INFO score
by
chrchang523
9.9k
If you aren't willing to provide more precise information than this, sufficient for a reader to reproduce what you're seeing, I will delete…
Answer: Error while trying to install salmon
by
Chris
▴ 10
Donwloading the package from conda (https://anaconda.org/conda-forge/boost/files?version=1.60.0) worked for me wget https://anaconda.org/…
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by
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First issue is that GEO series matrix files can't be read using `read.delim`. Second issue is the data are from Agilent microarrays and …
Comment: PLINK2 selecting variants based on INFO score
by
m.c.roozen
• 0
I have tried that (the .pvar file contains the "1:10586" form as ID which I mentioned above) which leads to the same output as above, 0 var…
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by
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You can run any system command from inside R using `system()`. This works well if there is a single command without many dependencies. For …
Comment: samtools markdup in Rsamtools
by
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152k
> But other solutions are also fine: bash, nextflow, snakemake
Answer: samtools markdup in Rsamtools
by
ATpoint
68k
My honest opinion: Do processing of sequencing data on the standard command line with samtools. There is no need for the added complexity t…
Comment: To batch correct or analyse separately?
by
predeus
★ 1.8k
Another great and up-to-date resource is this: https://www.sc-best-practices.org/preamble.html
Comment: PLINK2 selecting variants based on INFO score
by
chrchang523
9.9k
The --exclude file must use the same variant IDs as your .pvar file. You should elaborate on what seemed to go wrong when you tried to arr…
Comment: phylogeny
by
炫
• 0
Hello, my problem is the same as yours, did you finally solve this problem?
Comment: phylogeny
by
炫
• 0
您好,我的问题和您的一模一样,请问您这个问题最终解决了吗
Comment: Issue with hmmcalibrate during tutorial.
by
apcreyes29
• 0
If that's the case then I'll just proceed then. Thank you!
Answer: To batch correct or analyse separately?
by
ATpoint
68k
Instead of writing that all down I recommend to read the relevant part of the Bioconductor scRNA-seq book (OSCA) which covers the "how's" a…
Answer: Issue with hmmcalibrate during tutorial.
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Mensur Dlakic
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Pretty sure that `hmmcalibrate` does not exist in HMMer version 3+ as the models are internally calibrated. I think you are using a manual …
Comment: High downstream gene expression
by
yoser4
▴ 10
Thank you for your reply. Your answer has helped me. I am a novice in scientific research, and the reading of literature is really poor. …
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