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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
1
reply
154
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 3 days ago by
GenoMax
141k • written 3 days ago by
eesiribloom
▴ 80
0
votes
0
replies
119
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
3 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
121
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
3 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
130
views
FreeBayes detection capacity
reads
freebayes
long
3 days ago by
quentinperriere
• 0
0
votes
2
replies
206
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
1 day ago by
DKA
▴ 40
0
votes
2
replies
227
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
3 days ago by
rj.rezwan
• 0
0
votes
0
replies
147
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
4 days ago by
Hien
• 0
0
votes
2
replies
257
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
2 days ago by
Koketso
• 0
0
votes
0
replies
173
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 4 days ago by
Ram
43k • written 4 days ago by
menyawino
• 0
1
vote
3
replies
304
views
Ensembl gene id conversion
biomart
ensembl
updated 2 days ago by
ATpoint
81k • written 4 days ago by
naveedhasan2000
• 0
1
vote
2
replies
287
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 3 days ago by
Istvan Albert
100k • written 4 days ago by
Jiang
• 0
0
votes
0
replies
172
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
5 days ago by
YiweiZhu
▴ 30
0
votes
0
replies
176
views
Somatic and Germline variant calling for tumor, normal and blood sample
germline
variants
somatic
updated 4 days ago by
Ram
43k • written 5 days ago by
anitharavichandran2211
• 0
0
votes
1
reply
218
views
Ciriquant not configuring hisat2 indexed files
ciriquant
updated 5 days ago by
Carlo Yague
8.6k • written 5 days ago by
Atul K.
• 0
0
votes
2
replies
296
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
5 days ago by
O.rka
▴ 710
0
votes
6
replies
508
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
3 days ago by
Dunois
★ 2.5k
4
votes
7
replies
523
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 4 days ago by
Ram
43k • written 6 days ago by
AHerik
▴ 20
0
votes
0
replies
170
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 6 days ago by
GenoMax
141k • written 6 days ago by
zec018
• 0
0
votes
0
replies
185
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 6 days ago by
Ram
43k • written 6 days ago by
roussine
▴ 10
0
votes
0
replies
168
views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
ATAC-seq
HOMER
6 days ago by
Ronin
• 0
4
votes
13
replies
756
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 1 day ago by
BioinfGuru
★ 1.7k • written 7 days ago by
matteo.levorato
• 0
2
votes
1
reply
233
views
VEP annotation --per_gene allele choice
VEP
updated 6 days ago by
Ram
43k • written 6 days ago by
atariw
▴ 10
0
votes
2
replies
267
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 6 days ago by
Apollonia
• 0
1
vote
1
reply
234
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 6 days ago by
Ram
43k • written 6 days ago by
Fish
• 0
0
votes
0
replies
176
views
Snakemake fails to find conda in PBS
snakemake
6 days ago by
yixinzeng
• 0
0
votes
0
replies
181
views
KaryoPlot: Gene coverage over centromeric regions
Gene
coverage
Centromere
Bedtools
6 days ago by
Mary
• 0
0
votes
0
replies
170
views
Protein stability analysis
mutation
analysis
6 days ago by
marco.barr
▴ 60
1
vote
4
replies
372
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 5 days ago by
BioinfGuru
★ 1.7k • written 6 days ago by
Morteza
• 0
3
votes
1
reply
254
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 6 days ago by
Ram
43k • written 6 days ago by
rj.rezwan
• 0
0
votes
0
replies
159
views
Multiple Spike-Ins
MeRIP
Spike-In
7 days ago by
Adam
▴ 20
0
votes
0
replies
155
views
Tools for Sequence Consensus
Consensus-Sequence
bacteria
updated 7 days ago by
Ram
43k • written 7 days ago by
Reno
• 0
2
votes
2
replies
264
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 7 days ago by
ATpoint
81k • written 7 days ago by
Shicheng Guo
★ 9.4k
1
vote
0
replies
146
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
7 days ago by
eesiribloom
▴ 80
0
votes
3
replies
297
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 5 days ago by
ATpoint
81k • written 7 days ago by
gdfsnkfns
• 0
0
votes
4
replies
287
views
Questions about transfering wgs file to reference genome file
fasta
cram
genome
7 days ago by
me
• 0
0
votes
2
replies
247
views
WGCNA
PCA
WGCNA
EIGENGENE
6 days ago by
rajasekargutha
▴ 60
0
votes
3
replies
245
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 7 days ago by
GenoMax
141k • written 7 days ago by
neish
• 0
1
vote
0
replies
147
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 7 days ago by
Ram
43k • written 7 days ago by
ian.will
▴ 30
0
votes
0
replies
100
views
Surrogate variable analysis for paired RNA seq experiment
sva
rnaseq
ruvseq
7 days ago by
nhaus
▴ 300
1
vote
3
replies
253
views
True variants selection
vcf
bcftools
updated 6 days ago by
dthorbur
★ 1.9k • written 7 days ago by
maevalefeuvre
• 0
0
votes
1
reply
149
views
How to reveal real AF of variant if duplicates can't be removed (such as in amplicon-seq)
allele-frequency
amplicon-seq
updated 7 days ago by
Ram
43k • written 7 days ago by
CY
▴ 750
0
votes
0
replies
95
views
Creating a BSgenome data package from a NCBI assembly - Virus
Virus
BSgenomeForge
BSgenome
R
7 days ago by
JirMan
▴ 20
1
vote
1
reply
161
views
Failed to download data from EBI with ascp
EBI
aspera
updated 7 days ago by
GenoMax
141k • written 7 days ago by
biock
▴ 60
0
votes
0
replies
388
views
BETA whether on the same scale when performing rank-based inverse normal transformation on the same type of phenotype data for two cohorts separately…
normal
inverse
transformation
7 days ago by
Isaac
• 0
0
votes
0
replies
99
views
Combining VG graphs
vg
graphs
combine
7 days ago by
AshleeThomson
▴ 70
0
votes
0
replies
101
views
Installing SALSA and HIRise scafolding software
scafolding
SALSA
genome-assembly
HIRise
updated 7 days ago by
Ram
43k • written 7 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
172
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA
substitution
VCFstats
Evolution
VCF
updated 7 days ago by
Pierre Lindenbaum
161k • written 7 days ago by
Saran
▴ 50
0
votes
2
replies
254
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
5 days ago by
ramin.k2013
• 0
0
votes
0
replies
151
views
Normalization in Metagenomics Sequencing By Total Number of Reads: Pre- or Post-Filtering and the Role of Unclassified Reads
Normalization
Metagenomics
updated 7 days ago by
Ram
43k • written 8 days ago by
ramin.k2013
• 0
0
votes
1
reply
151
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
updated 8 days ago by
Pierre Lindenbaum
161k • written 8 days ago by
sainavyav22
• 0
1,000 results • Page
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Recent Votes
Answer: Bedtools nuc : calculating the GC content in a sliding window
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
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141k
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★ 1.2k
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Recent Replies
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
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…
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