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1,000 results • Page
1 of 20
Sort: Votes
Rank
Views
Votes
Replies
41
votes
55
replies
12k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
8.0 years ago by
midox
▴ 290
28
votes
17
replies
21k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
2.4 years ago by
Leite
★ 1.3k
24
votes
25
replies
8.1k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.7 years ago by
dpc
▴ 240
23
votes
22
replies
49k
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 16 months ago by
Nicole
• 0 • written 5.9 years ago by
gaelgarcia
▴ 260
23
votes
10
replies
5.8k
views
How to predict individual ethnicity information by using hapmap data
SNP
Ethnicity
Hapmap
updated 3.0 years ago by
Kevin Blighe
87k • written 6.1 years ago by
Joe
▴ 40
22
votes
19
replies
3.2k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.5 years ago by
zizigolu
★ 4.3k
22
votes
20
replies
2.5k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 12 months ago by
Ram
43k • written 7.8 years ago by
Farbod
★ 3.4k
20
votes
17
replies
6.0k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
6.7 years ago by
Anand Rao
▴ 630
20
votes
15
replies
29k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 20 months ago by
Ram
43k • written 8.3 years ago by
dam4l
▴ 200
20
votes
17
replies
3.2k
views
How to add "transcript" feature to a gtf file?
gtf
updated 9 months ago by
1769mkc
★ 1.2k • written 3.2 years ago by
pomodoro_sinensis
▴ 110
19
votes
43
replies
5.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.7 years ago by
nazaninhoseinkhan
▴ 520
18
votes
7
replies
1.4k
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2
Variable
RNA-seq
19 months ago by
Rafael Soler
★ 1.2k
18
votes
19
replies
2.3k
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 16 months ago by
Ram
43k • written 5.3 years ago by
rbkh09
• 0
18
votes
4
replies
8.7k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 13 months ago by
Ram
43k • written 10.7 years ago by
user
▴ 940
17
votes
8
replies
2.3k
views
Number of unique authors in PubMed in last 10 years
PubMed
8.1 years ago by
nejc
▴ 50
17
votes
19
replies
2.8k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.6 years ago by
Gian77
▴ 60
17
votes
13
replies
6.5k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment
genome
sequencing
6.9 years ago by
lghust2011
▴ 110
17
votes
37
replies
4.7k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.9 years ago by
Biostar
20 • written 5.0 years ago by
williamsbrian5064
▴ 510
16
votes
16
replies
3.1k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
6.1 years ago by
bioinfo456
▴ 150
16
votes
14
replies
17k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
5.8 years ago by
salamandra
▴ 550
16
votes
17
replies
3.2k
views
6 follow
RNA seq pipeline
RNA-Seq
6.5 years ago by
dimitrischat
▴ 210
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 24 months ago by
Ram
43k • written 9.2 years ago by
Mo
▴ 920
16
votes
10
replies
5.6k
views
6 follow
Powerful desktop computer for genomics
next-gen
sequencing
ChIP-Seq
RNA-Seq
7.9 years ago by
Alternative
▴ 270
16
votes
21
replies
2.2k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
7.5 years ago by
Farbod
★ 3.4k
16
votes
18
replies
5.4k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.6 years ago by
Mensur Dlakic
★ 27k • written 4.6 years ago by
tikshyadav19
• 0
15
votes
14
replies
3.2k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
6.3 years ago by
John
▴ 270
15
votes
16
replies
1.7k
views
ncbi error report log for validate fastq issue
sra-tools
updated 6 months ago by
GenoMax
141k • written 6 months ago by
1769mkc
★ 1.2k
15
votes
19
replies
1.9k
views
trimmomaric command for a fasta file?
trimmomatic
updated 6.0 years ago by
Ram
43k • written 6.0 years ago by
Nadin.asal
• 0
15
votes
14
replies
1.9k
views
how can interpret these biologically weird results?
RNA-Seq
updated 3.2 years ago by
Biostar
20 • written 6.4 years ago by
Mozart
▴ 330
14
votes
8
replies
5.0k
views
Unable To Replicate Splice Junction In Tophat
tophat2
bam
10.5 years ago by
Dan D
7.4k
14
votes
18
replies
2.1k
views
Clustering in single cell
seurat
single-cell
updated 6 months ago by
e.r.zakiev
▴ 190 • written 6 months ago by
Chris
▴ 260
14
votes
30
replies
3.4k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
4.9 years ago by
Malka
▴ 80
14
votes
18
replies
4.9k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 7.3 years ago by
Biostar
20 • written 7.5 years ago by
plink_9857
▴ 50
14
votes
5
replies
3.1k
views
bioinformatics basic training
genome
updated 13 months ago by
Ram
43k • written 9.4 years ago by
f.muoghalu
• 0
14
votes
10
replies
877
views
How to remove center population from seurat cluster
single-cell
4 months ago by
synat.keam
▴ 100
14
votes
16
replies
1.9k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 3.4 years ago by
lieven.sterck
15k • written 3.4 years ago by
utsafar
▴ 80
13
votes
7
replies
6.5k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray
NA
genesymbol
updated 7.4 years ago by
Biostar
20 • written 7.4 years ago by
Raheleh
▴ 260
13
votes
11
replies
7.2k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq
QC
5.5 years ago by
jackgrayner
▴ 80
13
votes
16
replies
6.0k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
7.3 years ago by
Paul
★ 1.5k
13
votes
13
replies
9.0k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 6.1 years ago by
Devon Ryan
104k • written 6.1 years ago by
amitgourav.ghosh12
▴ 70
13
votes
6
replies
4.0k
views
bcftools isec -n operators
bcftools
intersect
updated 2.6 years ago by
Ram
43k • written 4.3 years ago by
Begonia_pavonina
▴ 150
13
votes
4
replies
23k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage
depth
read depth
7.0 years ago by
ariel.balter
▴ 260
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 1 day ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
13
votes
16
replies
7.2k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
5.3 years ago by
DNAngel
▴ 250
13
votes
19
replies
5.3k
views
bbmerge not joining paired-end reads
bbmerge
alignment
6.4 years ago by
bioplanet
▴ 60
13
votes
13
replies
1.5k
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility
sanger sequencing
variants
4.5 years ago by
DanielC
▴ 170
13
votes
24
replies
4.5k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 7.1 years ago by
GenoMax
141k • written 7.1 years ago by
Gary
▴ 480
13
votes
13
replies
17k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
4.7 years ago by
Arindam Ghosh
▴ 510
12
votes
11
replies
3.2k
views
How To Get Snp Genotypes
snp
genotyping
updated 12.6 years ago by
Lars Juhl Jensen
11k • written 13.0 years ago by
Pri
▴ 20
12
votes
12
replies
4.9k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 10.4 years ago by
Istvan Albert
100k • written 10.4 years ago by
biolab
★ 1.4k
1,000 results • Page
1 of 20
Recent Votes
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Comment: Questions about a bug when transferring cram file to bam file
A: Out Of Disk Space With Picard Tools ?
Exporting WGCNA step-to-step network construction objects into igraph object
Answer: Downloaded pdb's on rcsb.org
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Recent Replies
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
BioinfGuru
★ 1.7k
great guidance ... thank you
Comment: error in CPC2
by
Ram
43k
Ashok, what is CPC2? Please edit your post and add as much context as you can.
Comment: python file for cpc2
by
Ram
43k
Ashok - someone else had to (guess and) add context to your post. Please give us as much information as you can in the first place - we can…
Comment: python file for cpc2
by
Pierre Lindenbaum
161k
https://academic.oup.com/nar/article/45/W1/W12/3831091 > CPC2: a fast and accurate coding potential calculator based on sequence intrinsic…
Comment: error in CPC2
by
GenoMax
141k
Looks like you are running code that was written for `python v.2.x` but you probably have `python v.3.x` or a newer version than `python v.…
Comment: Per base sequence content failed miserably
by
GenoMax
141k
If this is 16S sequencing just follow the standard workflows like Qiime2.https://docs.qiime2.org/2024.2/tutorials/overview/
Comment: Out Of Disk Space With Picard Tools ?
by
kjngo
• 0
Thanks changing the tmp dir fixed the out of disk space error for me as well.
Answer: Downloaded pdb's on rcsb.org
by
GenoMax
141k
Download services for PDB are described on this page: https://www.rcsb.org/docs/programmatic-access/file-download-services It could be as …
Answer: How to compare the quality of assemblies
by
shelkmike
★ 1.2k
Since BUSCO results are almost identical but the assembly sizes differ significantly, I suppose that the difference between the assemblies …
Comment: differential gene expression analysis when not all samples have an untreated cou
by
nhaus
▴ 300
Thank you very much for your answer, that was very helpful! > Impossible to say. It depends on your data, particularly on how the donors …
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
bk11
★ 2.3k
This could be because they are probably merging two or more datasets. If you are merging two or more datasets, it will be very important th…
Answer: Problem with Mirdeep2 and Randfold output
by
otieno43
▴ 30
I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file
by
GenoMax
141k
Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle
by
Ram
43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
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