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1,000 results • Page
1 of 20
Sort: Votes
Rank
Views
Votes
Replies
41
votes
55
replies
9.6k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
6.8 years ago by
midox
▴ 290
27
votes
17
replies
16k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
14 months ago by
Leite
★ 1.2k
24
votes
25
replies
5.4k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
2.5 years ago by
dpc
▴ 240
23
votes
22
replies
36k
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 9 weeks ago by
Nicole
• 0 • written 4.7 years ago by
gaelgarcia
▴ 250
23
votes
10
replies
4.9k
views
How to predict individual ethnicity information by using hapmap data
SNP
Ethnicity
Hapmap
updated 21 months ago by
Kevin Blighe
84k • written 4.9 years ago by
Joe
▴ 40
22
votes
19
replies
2.4k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
6.3 years ago by
fi1d18
★ 4.1k
22
votes
20
replies
2.0k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
RNA-Seq
blast
gene
genome
Forum
6.6 years ago by
Farbod
★ 3.3k
19
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 6 months ago by
Ram
37k • written 7.1 years ago by
dam4l
▴ 180
19
votes
43
replies
3.9k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.5 years ago by
nazaninhoseinkhan
▴ 490
18
votes
19
replies
1.5k
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
updated 9 weeks ago by
Ram
37k • written 4.1 years ago by
rbkh09
• 0
18
votes
7
replies
745
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2
Variable
RNA-seq
4 months ago by
Rafael Soler
★ 1.1k
18
votes
4
replies
8.0k
views
How To Find Rna-Seq Data Of Published Papers?
bioinformatics
next-gen
rna-seq
geo
9.5 years ago by
user
▴ 930
17
votes
19
replies
2.0k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.4 years ago by
Gian77
▴ 60
17
votes
37
replies
3.2k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 3.7 years ago by
Biostar
20 • written 3.8 years ago by
williamsbrian5064
▴ 470
17
votes
13
replies
5.3k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
5.7 years ago by
lghust2011
▴ 100
17
votes
8
replies
1.8k
views
Number of unique authors in PubMed in last 10 years
PubMed
6.9 years ago by
nejc
▴ 50
16
votes
14
replies
13k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
4.6 years ago by
salamandra
▴ 510
16
votes
8
replies
1.6k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
problem
unresolved
bioinformatics
updated 6.3 years ago by
Biostar
20 • written 6.3 years ago by
chen
★ 2.4k
16
votes
10
replies
4.6k
views
6 follow
Powerful desktop computer for genomics
next-gen
sequencing
ChIP-Seq
RNA-Seq
6.7 years ago by
Alternative
▴ 270
16
votes
21
replies
1.5k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
6.3 years ago by
Farbod
★ 3.3k
16
votes
16
replies
2.3k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
4.9 years ago by
bioinfo456
▴ 150
16
votes
18
replies
3.5k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.4 years ago by
Mensur Dlakic
★ 22k • written 3.4 years ago by
tikshyadav19
• 0
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 9 months ago by
Ram
37k • written 8.0 years ago by
Mo
▴ 920
16
votes
17
replies
2.6k
views
6 follow
RNA seq pipeline
RNA-Seq
5.3 years ago by
dimitrischat
▴ 180
15
votes
14
replies
2.2k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
5.1 years ago by
John
▴ 260
15
votes
14
replies
1.3k
views
how can interpret these biologically weird results?
RNA-Seq
updated 2.0 years ago by
Biostar
20 • written 5.2 years ago by
Mozart
▴ 330
15
votes
19
replies
1.3k
views
trimmomaric command for a fasta file?
trimmomatic
updated 4.8 years ago by
Ram
37k • written 4.8 years ago by
Nadin.asal
• 0
14
votes
17
replies
4.8k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
5.5 years ago by
Anand Rao
▴ 550
14
votes
8
replies
4.5k
views
Unable To Replicate Splice Junction In Tophat
tophat2
bam
9.3 years ago by
Dan D
7.4k
14
votes
30
replies
2.4k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
3.7 years ago by
Malka
▴ 70
14
votes
18
replies
4.0k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.1 years ago by
Biostar
20 • written 6.3 years ago by
plink_9857
▴ 50
14
votes
5
replies
2.6k
views
bioinformatics basic training
genome
Tutorial
updated 11 months ago by
Ram
37k • written 8.2 years ago by
f.muoghalu
• 0
14
votes
16
replies
1.2k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 2.2 years ago by
lieven.sterck
14k • written 2.2 years ago by
utsafar
▴ 80
13
votes
7
replies
5.7k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray
NA
genesymbol
updated 6.2 years ago by
Biostar
20 • written 6.2 years ago by
Raheleh
▴ 230
13
votes
6
replies
9.6k
views
6 follow
MAF vs VAF
sequencing
4.9 years ago by
lauren.wahyudi
▴ 40
13
votes
22
replies
8.7k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 5.4 years ago by
Biostar
20 • written 5.6 years ago by
lessismore
★ 1.3k
13
votes
13
replies
922
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility
sanger sequencing
variants
3.3 years ago by
DanielC
▴ 160
13
votes
16
replies
4.8k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
6.1 years ago by
Paul
★ 1.5k
13
votes
24
replies
3.2k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 5.9 years ago by
GenoMax
125k • written 5.9 years ago by
Gary
▴ 480
13
votes
16
replies
5.2k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
4.1 years ago by
DNAngel
▴ 240
13
votes
19
replies
4.1k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.2 years ago by
bioplanet
▴ 60
13
votes
13
replies
7.7k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 4.9 years ago by
Devon Ryan
102k • written 4.9 years ago by
amitgourav.ghosh12
▴ 70
12
votes
28
replies
1.8k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
4.7 years ago by
Za
▴ 140
12
votes
11
replies
2.7k
views
How To Get Snp Genotypes
snp
genotyping
updated 11.4 years ago by
Lars Juhl Jensen
11k • written 11.8 years ago by
Pri
▴ 20
12
votes
8
replies
546
views
Align 16S sequence to a reference
16S
sequence
alignment
updated 4 months ago by
Matthias Zepper
2.9k • written 4 months ago by
A_heath
▴ 120
12
votes
8
replies
2.5k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence
RNA-Seq
6.0 years ago by
statfa
▴ 680
12
votes
14
replies
4.1k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
4.0 years ago by
star
▴ 330
12
votes
10
replies
3.5k
views
Speed up BLASTp vs NCBI nr database
blast
6.7 years ago by
biotech
▴ 560
12
votes
17
replies
3.8k
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
5.3 years ago by
anonymous1192976466
▴ 50
12
votes
12
replies
4.4k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 9.2 years ago by
Istvan Albert
96k • written 9.2 years ago by
biolab
★ 1.4k
1,000 results • Page
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Deseq2 with one factor and multiple levels
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1000 genomes project reference panel - GRCh38
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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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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
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Answer: samtools markdup in Rsamtools
by
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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
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★ 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
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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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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
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▴ 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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