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1,000 results • Page
1 of 20
Sort: Votes
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Views
Votes
Replies
41
votes
55
replies
8.9k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
6.4 years ago by
midox
▴ 290
27
votes
17
replies
14k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
8 months ago by
Leite
★ 1.2k
24
votes
25
replies
4.5k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
2.1 years ago by
dpc
▴ 240
23
votes
21
replies
31k
views
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
4.3 years ago by
gaelgarcia
▴ 250
23
votes
10
replies
4.7k
views
How to predict individual ethnicity information by using hapmap data
SNP
Ethnicity
Hapmap
updated 16 months ago by
Kevin Blighe
82k • written 4.5 years ago by
Joe
▴ 40
22
votes
20
replies
1.8k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
RNA-Seq
blast
gene
genome
Forum
6.1 years ago by
Farbod
★ 3.3k
22
votes
19
replies
2.2k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
5.9 years ago by
Angel
★ 4.1k
19
votes
43
replies
3.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.0 years ago by
nazaninhoseinkhan
▴ 430
18
votes
4
replies
7.7k
views
How To Find Rna-Seq Data Of Published Papers?
bioinformatics
next-gen
rna-seq
geo
9.0 years ago by
user
▴ 870
18
votes
19
replies
1.4k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
3.6 years ago by
rbkh09
• 0
17
votes
8
replies
1.6k
views
Number of unique authors in PubMed in last 10 years
PubMed
6.4 years ago by
nejc
▴ 50
17
votes
13
replies
4.8k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
5.3 years ago by
lghust2011
▴ 100
17
votes
37
replies
2.8k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 3.2 years ago by
Biostar
20 • written 3.4 years ago by
williamsbrian5064
▴ 430
17
votes
19
replies
1.8k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.0 years ago by
Gian77
▴ 60
16
votes
21
replies
1.3k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
5.9 years ago by
Farbod
★ 3.3k
16
votes
18
replies
2.7k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.0 years ago by
Mensur Dlakic
★ 20k • written 3.0 years ago by
tikshyadav19
• 0
16
votes
14
replies
12k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
4.1 years ago by
salamandra
▴ 500
16
votes
10
replies
4.4k
views
6 follow
Powerful desktop computer for genomics
next-gen
sequencing
ChIP-Seq
RNA-Seq
6.2 years ago by
Alternative
▴ 270
16
votes
8
replies
1.5k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
problem
unresolved
bioinformatics
updated 5.8 years ago by
Biostar
20 • written 5.9 years ago by
chen
★ 2.4k
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 3 months ago by
Ram
36k • written 7.5 years ago by
Mo
▴ 920
16
votes
16
replies
2.1k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
4.4 years ago by
Uday Rangaswamy
▴ 150
16
votes
17
replies
2.4k
views
6 follow
RNA seq pipeline
RNA-Seq
4.8 years ago by
dimitrischat
▴ 180
15
votes
14
replies
1.9k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
4.6 years ago by
John
▴ 240
15
votes
15
replies
23k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 16 days ago by
Ram
36k • written 6.6 years ago by
dam4l
▴ 180
15
votes
19
replies
1.1k
views
trimmomaric command for a fasta file?
trimmomatic
updated 4.3 years ago by
Ram
36k • written 4.3 years ago by
Nadin.asal
• 0
15
votes
14
replies
1.2k
views
how can interpret these biologically weird results?
RNA-Seq
updated 19 months ago by
Biostar
20 • written 4.8 years ago by
Mozart
▴ 320
14
votes
17
replies
4.5k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
5.0 years ago by
Anand Rao
▴ 520
14
votes
8
replies
4.4k
views
Unable To Replicate Splice Junction In Tophat
tophat2
bam
8.9 years ago by
Dan D
7.3k
14
votes
5
replies
2.5k
views
bioinformatics basic training
genome
Tutorial
updated 5 months ago by
Ram
36k • written 7.7 years ago by
f.muoghalu
• 0
14
votes
16
replies
1.0k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 21 months ago by
lieven.sterck
14k • written 21 months ago by
utsafar
▴ 80
14
votes
18
replies
3.8k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 5.6 years ago by
Biostar
20 • written 5.8 years ago by
plink_9857
▴ 50
14
votes
30
replies
2.1k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
3.3 years ago by
Malka
▴ 70
13
votes
7
replies
5.3k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray
NA
genesymbol
updated 5.7 years ago by
Biostar
20 • written 5.8 years ago by
Raheleh
▴ 230
13
votes
13
replies
7.3k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 4.4 years ago by
Devon Ryan
102k • written 4.4 years ago by
amitgourav.ghosh12
▴ 70
13
votes
13
replies
797
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility
sanger sequencing
variants
2.8 years ago by
DanielC
▴ 150
13
votes
24
replies
2.8k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 5.4 years ago by
GenoMax
119k • written 5.4 years ago by
Gary
▴ 480
13
votes
19
replies
3.7k
views
bbmerge not joining paired-end reads
bbmerge
alignment
4.7 years ago by
bioplanet
▴ 60
13
votes
16
replies
4.6k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
3.6 years ago by
DNAngel
▴ 210
13
votes
6
replies
8.8k
views
6 follow
MAF vs VAF
sequencing
4.4 years ago by
lauren.wahyudi
▴ 40
13
votes
16
replies
4.5k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
5.6 years ago by
Paul
★ 1.4k
13
votes
22
replies
8.1k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 4.9 years ago by
Biostar
20 • written 5.1 years ago by
lessismore
★ 1.2k
12
votes
28
replies
1.5k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
4.2 years ago by
Za
▴ 140
12
votes
11
replies
2.6k
views
How To Get Snp Genotypes
snp
genotyping
updated 11.0 years ago by
Lars Juhl Jensen
11k • written 11.4 years ago by
Pri
▴ 20
12
votes
13
replies
2.0k
views
Gene Expression and Systems Biology (homework)
gene
homework
7.1 years ago by
sarathkurichiyil
• 0
12
votes
8
replies
2.3k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence
RNA-Seq
5.6 years ago by
statfa
▴ 660
12
votes
10
replies
3.3k
views
Speed up BLASTp vs NCBI nr database
blast
6.2 years ago by
biotech
▴ 560
12
votes
10
replies
2.0k
views
7 follow
SAM / BAM alignments
SAM
BAM
5.6 years ago by
John
13k
12
votes
12
replies
4.2k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 8.7 years ago by
Istvan Albert
94k • written 8.7 years ago by
biolab
★ 1.4k
12
votes
17
replies
3.5k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python
Newick
phylogenetics
tree
phylogeny
4.9 years ago by
anonymous1192976466
▴ 50
12
votes
14
replies
3.5k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
3.5 years ago by
star
▴ 290
1,000 results • Page
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Recent Votes
Answer: How to read vcf file in python?
Comment: Gene-based and transcriptome-based profiling
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Answer: Installing ensembl-vep
Answer: Installing ensembl-vep
Answer: Changing the x-axis in ggseqlogo in R
Answer: Best way to detect CNV using WGS data
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Answer: Problem in MarkDuplicates of picard
by
Pierre Lindenbaum
148k
VN in ` VN: ` should have a value. The htsjdk library _requires_ a value here: https://github.com/gkno/picard/blob/ffb68b5183efdaa561…
Comment: Gene-based and transcriptome-based profiling
by
Chris
• 0
May I chat with you somewhere for more detail?
Answer: Is it possible to make certain branches of Snakemake conditional?
by
edsouza
▴ 30
Commenting to update: it seems that this issue is solved not at the level of the program, but at the level of the command line. `snakemake …
Comment: using gatk haplotypecaller for variants extraction
by
Nemo
• 0
thanks @Ram, yes I searched for my question, and I read the link you sent. As I found I can use gatk haplotypecaller (I am skeptical yet) b…
Comment: How to deal with `'select()' returned 1:many mapping between keys and columns` w
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640
> Is it because some genes do not have entrez ID? Yes. > If so, how should I deal with it? If you strictly require entrez IDs, then you…
Comment: using gatk haplotypecaller for variants extraction
by
Ram
36k
> I see the sample commands but I noticed they are for DNA seq data. So, it means I cannot use gatk haplotypecaller for rna seq data? You…
Comment: How to use RSEM to quantify genes and transcript expression from STAR outpute fi
by
Ram
36k
The "what is this supposed to be" part is the output prefix. Are you using `>&` when you mean to use `&>`? In any case, use `>rsem.out 2>rs…
Comment: Gene-based and transcriptome-based profiling
by
GenoMax
119k
It may be a case of semantics. When arrays were popular in early 2000s, people used the term "gene-based profiling". Both cases one is look…
Comment: Changing the x-axis in ggseqlogo in R
by
Ram
36k
I've moved the comment to an answer. Please accept it to mark the post as solved.
Comment: Changing the x-axis in ggseqlogo in R
by
margo
▴ 40
Thank you! That works!
Answer: Changing the x-axis in ggseqlogo in R
by
rpolicastro
9.4k
Untested but adding `+ scale_x_continuous(breaks=1:21, labels=-10:10)` to the returned ggplot2 object should work.
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by
tomas4482
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You can either create a new environment using Anaconda3 and download it via `conda install -n vep -c bioconda ensembl-vep` or install every…
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Thank you so much for detailed answer! I am not confused about transcriptome-base profiling because I think it is RNA-Seq analysis. I only …
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If you're comfortable using R, you can load the `.bed` files as tab delimited files, then `full_join` using `chr`, `start`, and `stop` as y…
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Its not that we don't know which transcripts are poly-adenylated and which arn't - its just that that information is not encoded in the gen…
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