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1,000 results • Page
1 of 20
Sort: Votes
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Views
Votes
Replies
41
votes
55
replies
11k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
7.5 years ago by
midox
▴ 290
27
votes
17
replies
19k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
22 months ago by
Leite
★ 1.2k
24
votes
25
replies
7.0k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.2 years ago by
dpc
▴ 240
23
votes
22
replies
43k
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 10 months ago by
Nicole
• 0 • written 5.4 years ago by
gaelgarcia
▴ 250
23
votes
10
replies
5.3k
views
How to predict individual ethnicity information by using hapmap data
SNP
Ethnicity
Hapmap
updated 2.4 years ago by
Kevin Blighe
86k • written 5.6 years ago by
Joe
▴ 40
22
votes
20
replies
2.2k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 5 months ago by
Ram
40k • written 7.2 years ago by
Farbod
★ 3.4k
22
votes
19
replies
2.7k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.0 years ago by
fi1d18
★ 4.2k
20
votes
17
replies
5.5k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
6.1 years ago by
Anand Rao
▴ 570
20
votes
17
replies
2.4k
views
How to add "transcript" feature to a gtf file?
gtf
updated 12 weeks ago by
1769mkc
★ 1.1k • written 2.7 years ago by
pomodoro_sinensis
▴ 110
20
votes
15
replies
28k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 14 months ago by
Ram
40k • written 7.7 years ago by
dam4l
▴ 190
19
votes
43
replies
4.7k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.1 years ago by
nazaninhoseinkhan
▴ 510
18
votes
19
replies
1.9k
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 10 months ago by
Ram
40k • written 4.7 years ago by
rbkh09
• 0
18
votes
7
replies
1.1k
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2
Variable
RNA-seq
12 months ago by
Rafael Soler
★ 1.2k
18
votes
4
replies
8.3k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 7 months ago by
Ram
40k • written 10.2 years ago by
user
▴ 940
17
votes
13
replies
6.0k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
6.4 years ago by
lghust2011
▴ 110
17
votes
19
replies
2.4k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.1 years ago by
Gian77
▴ 60
17
votes
8
replies
2.1k
views
Number of unique authors in PubMed in last 10 years
PubMed
7.5 years ago by
nejc
▴ 50
17
votes
37
replies
3.9k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.3 years ago by
Biostar
20 • written 4.5 years ago by
williamsbrian5064
▴ 480
16
votes
18
replies
4.7k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.1 years ago by
Mensur Dlakic
★ 25k • written 4.1 years ago by
tikshyadav19
• 0
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 17 months ago by
Ram
40k • written 8.6 years ago by
Mo
▴ 920
16
votes
16
replies
2.7k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
5.5 years ago by
bioinfo456
▴ 150
16
votes
10
replies
5.1k
views
6 follow
Powerful desktop computer for genomics
next-gen
sequencing
ChIP-Seq
RNA-Seq
7.4 years ago by
Alternative
▴ 270
16
votes
21
replies
1.7k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
7.0 years ago by
Farbod
★ 3.4k
16
votes
17
replies
2.9k
views
6 follow
RNA seq pipeline
RNA-Seq
5.9 years ago by
dimitrischat
▴ 200
16
votes
14
replies
15k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
5.3 years ago by
salamandra
▴ 550
15
votes
14
replies
2.7k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
5.7 years ago by
John
▴ 270
15
votes
19
replies
1.6k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.4 years ago by
Ram
40k • written 5.4 years ago by
Nadin.asal
• 0
15
votes
16
replies
748
views
ncbi error report log for validate fastq issue
sra-tools
updated 3 days ago by
GenoMax
134k • written 3 days ago by
1769mkc
★ 1.1k
15
votes
14
replies
1.6k
views
how can interpret these biologically weird results?
RNA-Seq
updated 2.7 years ago by
Biostar
20 • written 5.9 years ago by
Mozart
▴ 330
14
votes
8
replies
4.7k
views
Unable To Replicate Splice Junction In Tophat
tophat2
bam
10.0 years ago by
Dan D
7.4k
14
votes
16
replies
1.6k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 2.9 years ago by
lieven.sterck
14k • written 2.9 years ago by
utsafar
▴ 80
14
votes
18
replies
4.5k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.7 years ago by
Biostar
20 • written 6.9 years ago by
plink_9857
▴ 50
14
votes
30
replies
2.9k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
4.4 years ago by
Malka
▴ 80
14
votes
5
replies
2.9k
views
bioinformatics basic training
genome
updated 6 months ago by
Ram
40k • written 8.8 years ago by
f.muoghalu
• 0
13
votes
7
replies
6.2k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray
NA
genesymbol
updated 6.8 years ago by
Biostar
20 • written 6.9 years ago by
Raheleh
▴ 260
13
votes
13
replies
1.2k
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility
sanger sequencing
variants
3.9 years ago by
DanielC
▴ 160
13
votes
16
replies
6.3k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
4.7 years ago by
DNAngel
▴ 240
13
votes
24
replies
3.9k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 6.6 years ago by
GenoMax
134k • written 6.6 years ago by
Gary
▴ 480
13
votes
16
replies
5.4k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
6.7 years ago by
Paul
★ 1.5k
13
votes
19
replies
4.8k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.8 years ago by
bioplanet
▴ 60
13
votes
13
replies
15k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
4.1 years ago by
Arindam Ghosh
▴ 510
13
votes
22
replies
9.7k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 6.0 years ago by
Biostar
20 • written 6.2 years ago by
lessismore
★ 1.3k
13
votes
6
replies
11k
views
6 follow
MAF vs VAF
sequencing
5.5 years ago by
lauren.wahyudi
▴ 40
13
votes
13
replies
8.4k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 5.6 years ago by
Devon Ryan
103k • written 5.6 years ago by
amitgourav.ghosh12
▴ 70
13
votes
11
replies
6.2k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq
QC
4.9 years ago by
jackgrayner
▴ 80
12
votes
17
replies
4.3k
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
6.0 years ago by
anonymous1192976466
▴ 50
12
votes
8
replies
2.9k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence
RNA-Seq
6.7 years ago by
statfa
▴ 740
12
votes
13
replies
2.4k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 9 months ago by
Ram
40k • written 8.2 years ago by
sarathkurichiyil
• 0
12
votes
14
replies
5.1k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
4.6 years ago by
star
▴ 350
12
votes
10
replies
3.9k
views
Speed up BLASTp vs NCBI nr database
blast
7.3 years ago by
biotech
▴ 570
1,000 results • Page
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Recent Votes
A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
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Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
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Comment: MAKER: WARNING: Could not get initialization lock. Trying Again...
by
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134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files
by
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35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
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by
Tully
• 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
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• 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File
by
Reem
• 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR
by
Trivas
★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies)
by
Jeremy Leipzig
21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
by
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
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by
Pierre Lindenbaum
157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output
by
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I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files
by
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157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output
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shelkmike
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I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
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ATpoint
77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
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