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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
2.0 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
4.2 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 15 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
5.8 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
13
replies
4.8k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
5.2 years ago by
lghust2011
▴ 100
17
votes
19
replies
1.8k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.0 years ago by
Gian77
▴ 60
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
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 3.3 years ago by
williamsbrian5064
▴ 430
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
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
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
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
17
replies
2.4k
views
6 follow
RNA seq pipeline
RNA-Seq
4.8 years ago by
dimitrischat
▴ 180
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
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
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 11 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 18 months ago by
Biostar
20 • written 4.8 years ago by
Mozart
▴ 320
14
votes
17
replies
4.4k
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
8.8 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 5.7 years ago by
Raheleh
▴ 220
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
19
replies
3.7k
views
bbmerge not joining paired-end reads
bbmerge
alignment
4.7 years ago by
bioplanet
▴ 60
13
votes
13
replies
7.2k
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
795
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
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
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
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
13
replies
2.0k
views
Gene Expression and Systems Biology (homework)
gene
homework
7.1 years ago by
sarathkurichiyil
• 0
12
votes
10
replies
2.0k
views
7 follow
SAM / BAM alignments
SAM
BAM
5.6 years ago by
John
13k
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
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
4.8 years ago by
anonymous1192976466
▴ 50
12
votes
11
replies
2.6k
views
How To Get Snp Genotypes
snp
genotyping
updated 10.9 years ago by
Lars Juhl Jensen
11k • written 11.3 years ago by
Pri
▴ 20
12
votes
10
replies
3.3k
views
Speed up BLASTp vs NCBI nr database
blast
6.2 years ago by
biotech
▴ 560
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
14
replies
3.4k
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 insert dbSNP in a database?
Answer: fgsea
Answer: Finding out if a query sequence is present in a read library / bam file (blast a
C: GTF based salmon index file for GRCh38
C: GTF based salmon index file for GRCh38
Answer: Has anybody managed to install and run GroopM lately?
How to integrate multiple data sets from microarray platform prior meta-analysis?
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Comment: Finding out if a query sequence is present in a read library / bam file (blast a
by
Pierre Lindenbaum
147k
what was the command line please ?
Comment: How to insert dbSNP in a database?
by
Pierre Lindenbaum
147k
2) not the same version of dbsnp, not the same build
Comment: How to insert dbSNP in a database?
by
magnolia
• 0
Thank you! 1) I need this because I want to connect all the data I need query via SQL. 2) Thanks a lot but this file only has 200 million…
Comment: The best way to get gene lengths for 15K+ genes?
by
rpolicastro
9.4k
You should first ensure that calculating TPMs like this is valid for your analysis. Proper TPMs generally need to be calculated from transc…
Comment: Finding out if a query sequence is present in a read library / bam file (blast a
by
chronotope
▴ 10
Hey! I tried the script, but I am getting this error: > SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaultin…
Comment: Expanding reference genome with alt loci and decoy sequences
by
appropiate
▴ 30
My criteria for whether it makes sense would be comparing MAPQ values for alignments when using reference genome vs expanded genome. If the…
Comment: Warning - longer object length is not a multiple of shorter object length
by
JACKY
▴ 10
Thanks! Do you also think my genelength calculation method is slumpy? What do you think about this approach? library (EDASeq) en…
Answer: Does Cellranger filter out doublet?
by
ATpoint
64k
FAQ: https://kb.10xgenomics.com/hc/en-us/articles/360001074271-Does-Cell-Ranger-automatically-exclude-doublets-
Comment: Expanding reference genome with alt loci and decoy sequences
by
ATpoint
64k
Yes, technically you can append any sequence to the reference followed by building a new index. If that makes sense or is appropriate is a …
Comment: Warning - longer object length is not a multiple of shorter object length
by
Michael Dondrup
52k
for example edgeR see https://support.bioconductor.org/p/64585/ Refer to https://www.biostars.org/p/115674/ , https://www.ncbi.nlm.nih.go…
Answer: How to insert dbSNP in a database?
by
Pierre Lindenbaum
147k
1) why do you need this ? 2) you can always upload the UCSC dbsnp files. ex.: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/databas…
Comment: Finding out if a query sequence is present in a read library / bam file (blast a
by
chronotope
▴ 10
thanks! I will try it out today
Comment: getting RPKM and VST using DEseq2 package
by
andrew.j.skelton73
6.4k
Check out [this][1] discussion on gene length in DESeq2. [1]: https://support.bioconductor.org/p/67131/
Comment: Warning - longer object length is not a multiple of shorter object length
by
JACKY
▴ 10
A proven Bioconductor package you mean using a package for normalization? If so, is there any package you recommend ?
Answer: MAKER AED score
by
lei
• 0
Did you adjust this setting in the maker_opts.ctl file? >pred_stats=1 #report AED and QI statistics for all predictions as well as models
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