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1,000 results • Page
1 of 20
Sort: Votes
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Views
Votes
Replies
41
votes
55
replies
9.8k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
7.0 years ago by
midox
▴ 290
27
votes
17
replies
16k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
15 months ago by
Leite
★ 1.2k
24
votes
25
replies
5.7k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
2.7 years ago by
dpc
▴ 240
23
votes
22
replies
38k
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 3 months ago by
Nicole
• 0 • written 4.9 years ago by
gaelgarcia
▴ 250
23
votes
10
replies
5.0k
views
How to predict individual ethnicity information by using hapmap data
SNP
Ethnicity
Hapmap
updated 23 months ago by
Kevin Blighe
84k • written 5.1 years ago by
Joe
▴ 40
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
6.7 years ago by
Farbod
★ 3.4k
22
votes
19
replies
2.4k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
6.5 years ago by
fi1d18
★ 4.1k
20
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 7 months ago by
Ram
38k • written 7.2 years ago by
dam4l
▴ 190
19
votes
43
replies
4.0k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.6 years ago by
nazaninhoseinkhan
▴ 500
18
votes
19
replies
1.6k
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 3 months ago by
Ram
38k • written 4.2 years ago by
rbkh09
• 0
18
votes
7
replies
806
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2
Variable
RNA-seq
6 months ago by
Rafael Soler
★ 1.1k
18
votes
4
replies
8.1k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 28 days ago by
Ram
38k • written 9.6 years ago by
user
▴ 930
17
votes
8
replies
1.8k
views
Number of unique authors in PubMed in last 10 years
PubMed
7.0 years ago by
nejc
▴ 50
17
votes
19
replies
2.1k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.6 years ago by
Gian77
▴ 60
17
votes
37
replies
3.3k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 3.8 years ago by
Biostar
20 • written 4.0 years ago by
williamsbrian5064
▴ 470
17
votes
13
replies
5.4k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
5.9 years ago by
lghust2011
▴ 100
16
votes
10
replies
4.7k
views
6 follow
Powerful desktop computer for genomics
next-gen
sequencing
ChIP-Seq
RNA-Seq
6.8 years ago by
Alternative
▴ 270
16
votes
17
replies
2.7k
views
6 follow
RNA seq pipeline
RNA-Seq
5.4 years ago by
dimitrischat
▴ 180
16
votes
14
replies
14k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
4.8 years ago by
salamandra
▴ 530
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 11 months ago by
Ram
38k • written 8.1 years ago by
Mo
▴ 920
16
votes
21
replies
1.6k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
6.5 years ago by
Farbod
★ 3.4k
16
votes
16
replies
2.4k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
5.0 years ago by
bioinfo456
▴ 150
16
votes
8
replies
1.6k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
problem
unresolved
bioinformatics
updated 6.4 years ago by
Biostar
20 • written 6.5 years ago by
chen
★ 2.4k
16
votes
18
replies
3.8k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.6 years ago by
Mensur Dlakic
★ 23k • written 3.6 years ago by
tikshyadav19
• 0
15
votes
14
replies
2.3k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
5.2 years ago by
John
▴ 270
15
votes
14
replies
1.4k
views
how can interpret these biologically weird results?
RNA-Seq
updated 2.2 years ago by
Biostar
20 • written 5.4 years ago by
Mozart
▴ 330
15
votes
19
replies
1.3k
views
trimmomaric command for a fasta file?
trimmomatic
updated 4.9 years ago by
Ram
38k • written 4.9 years ago by
Nadin.asal
• 0
14
votes
17
replies
4.9k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
5.6 years ago by
Anand Rao
▴ 550
14
votes
8
replies
4.6k
views
Unable To Replicate Splice Junction In Tophat
tophat2
bam
9.5 years ago by
Dan D
7.4k
14
votes
5
replies
2.7k
views
bioinformatics basic training
genome
updated 14 days ago by
Ram
38k • written 8.3 years ago by
f.muoghalu
• 0
14
votes
16
replies
1.3k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 2.4 years ago by
lieven.sterck
14k • written 2.4 years ago by
utsafar
▴ 80
14
votes
18
replies
4.1k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.2 years ago by
Biostar
20 • written 6.4 years ago by
plink_9857
▴ 50
14
votes
30
replies
2.5k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
3.9 years ago by
Malka
▴ 70
13
votes
7
replies
5.7k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray
NA
genesymbol
updated 6.3 years ago by
Biostar
20 • written 6.4 years ago by
Raheleh
▴ 250
13
votes
24
replies
3.3k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 6.0 years ago by
GenoMax
127k • written 6.0 years ago by
Gary
▴ 480
13
votes
6
replies
9.9k
views
6 follow
MAF vs VAF
sequencing
5.0 years ago by
lauren.wahyudi
▴ 40
13
votes
13
replies
7.8k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 5.1 years ago by
Devon Ryan
103k • written 5.1 years ago by
amitgourav.ghosh12
▴ 70
13
votes
16
replies
4.9k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
6.2 years ago by
Paul
★ 1.5k
13
votes
16
replies
5.4k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
4.2 years ago by
DNAngel
▴ 240
13
votes
19
replies
4.2k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.3 years ago by
bioplanet
▴ 60
13
votes
22
replies
8.8k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 5.5 years ago by
Biostar
20 • written 5.7 years ago by
lessismore
★ 1.3k
13
votes
13
replies
978
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility
sanger sequencing
variants
3.4 years ago by
DanielC
▴ 160
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 9.3 years ago by
Istvan Albert
97k • written 9.3 years ago by
biolab
★ 1.4k
12
votes
28
replies
1.8k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
4.8 years ago by
Za
▴ 140
12
votes
10
replies
3.6k
views
Speed up BLASTp vs NCBI nr database
blast
6.8 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
5.5 years ago by
anonymous1192976466
▴ 50
12
votes
8
replies
600
views
Align 16S sequence to a reference
16S
sequence
alignment
updated 6 months ago by
Matthias Zepper
3.4k • written 6 months ago by
A_heath
▴ 120
12
votes
8
replies
2.6k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence
RNA-Seq
6.2 years ago by
statfa
▴ 700
12
votes
10
replies
2.3k
views
7 follow
SAM / BAM alignments
SAM
BAM
6.2 years ago by
John
13k
12
votes
13
replies
2.1k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 3 months ago by
Ram
38k • written 7.7 years ago by
sarathkurichiyil
• 0
1,000 results • Page
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Recent Votes
smoothing or binning bigWig file
List of Ongoing and Planned Long Read Sequencing studies?
Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Answer: Read lengths greater than insert length
A: Changing Output From Gene ID to Symbol When Running findMarkers from Scran
Answer: BLAST Database error: No alias or index file found for nucleotide database
Answer: How to get gene from PSIBLAST resuts
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Recent Replies
Comment: split fasta file to train deep learning model
by
shenwei356
7.9k
Excluding sequences containing any letter not belonging to the 20 [amino acids letters](https://github.com/shenwei356/bio/blob/master/seq/a…
Comment: split fasta file to train deep learning model
by
pinheirofabiano
▴ 10
@shenwei356, thank you very much for your help, perfect! But now I realized that some fasta sequences contain the letter "B", which is ou…
Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
by
Mensur Dlakic
★ 23k
I think it depends on the speed of your local disks and the memory amount. On a single node, breaking up the database doesn't sound like a …
Comment: Sample size for population genetics
by
Jeremy Leipzig
21k
Other populations just make the model harder to generalize, not easier.
Comment: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
by
Vincent Laufer
★ 2.5k
i think there is some of that - my most upvoted comment of all time was a dismissive comment i made while extremely tired. for context i ha…
Comment: Molecular biologist / clinical pharmacologist (f/m/d)
by
Jeremy
▴ 770
Is this job on site in Vienna or remote?
Comment: smoothing or binning bigWig file
by
rls_08
▴ 40
if you use bigwigCompare , that would not create a sliding window, but instead, it will output the mean for each bin, according to the -bin…
Comment: Sample size for population genetics
by
zimmer.schweiz
• 0
Thank you so much for your answer. For common polygenic diseases, would it make sense to increase the number of populations sampled, in ord…
Answer: Sample size for population genetics
by
Jeremy Leipzig
21k
For a rare penetrant monogenic disease? A few cases. For a common polygenic disease or trait? 500k-10M
Answer: using GRanges metadata to constrain overlap searches between objects
by
seidel
11k
Rather than do all overlaps all the time for all samples, why not restrict the data by sample when you can. The code below works about 4 ti…
Comment: How to get gene from PSIBLAST resuts
by
Tom
• 0
Hello, thank you for your answer, I have a question, Why the information from the GFF file and from the feature table is different? I see …
Comment: SNP ID (rsID) to Chr no. and Position
by
Jewahir
• 0
Yeah, thank you for that!!
Comment: 1000 genomes hg38 with dbSNP rsid
by
Ram
38k
It should be pretty straightforward. Just to save you some pain, run these on the 1000g VCF once you download it: 1. `vt decompose -s` to …
Comment: 1000 genomes hg38 with dbSNP rsid
by
Vince
▴ 150
Yeah, I had some hope that I wouldn't need to mess with doing this ...
Answer: counting the unmapped reads
by
chemkhi.ali13
• 0
> Hi all, > > I have a sam file, my supervisor asked me to count the number of > unmapped reads, which command I should use? > > sam…
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