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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
238
views
RNAseq 1 control 2 different treatment
RNA-seq
3 days ago by
matteo.levorato
• 0
1
vote
0
replies
129
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 3 days ago by
Ram
43k • written 3 days ago by
Oscar
▴ 10
0
votes
0
replies
132
views
How should I make kallisto indexes?
kallisto
updated 3 days ago by
GenoMax
141k • written 3 days ago by
bioinfo
▴ 150
2
votes
0
replies
189
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
4 days ago by
Alexander
▴ 220
1
vote
1
reply
160
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 4 days ago by
GenoMax
141k • written 4 days ago by
eesiribloom
▴ 80
0
votes
0
replies
125
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
4 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
127
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
4 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
134
views
FreeBayes detection capacity
reads
freebayes
long
4 days ago by
quentinperriere
• 0
0
votes
2
replies
212
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
2 days ago by
DKA
▴ 40
0
votes
2
replies
233
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
3 days ago by
rj.rezwan
• 0
0
votes
0
replies
154
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
4 days ago by
Hien
• 0
0
votes
2
replies
261
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
2 days ago by
Koketso
• 0
0
votes
0
replies
180
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 4 days ago by
Ram
43k • written 5 days ago by
menyawino
• 0
1
vote
3
replies
311
views
Ensembl gene id conversion
biomart
ensembl
updated 3 days ago by
ATpoint
81k • written 5 days ago by
naveedhasan2000
• 0
1
vote
2
replies
290
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 3 days ago by
Istvan Albert
100k • written 5 days ago by
Jiang
• 0
0
votes
0
replies
174
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
6 days ago by
YiweiZhu
▴ 30
0
votes
0
replies
179
views
Somatic and Germline variant calling for tumor, normal and blood sample
germline
variants
somatic
updated 5 days ago by
Ram
43k • written 6 days ago by
anitharavichandran2211
• 0
0
votes
2
replies
301
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
513
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
525
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 5 days ago by
Ram
43k • written 6 days ago by
AHerik
▴ 20
0
votes
0
replies
173
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
187
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
170
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
772
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 2 days ago by
BioinfGuru
★ 1.7k • written 8 days ago by
matteo.levorato
• 0
2
votes
1
reply
236
views
VEP annotation --per_gene allele choice
VEP
updated 6 days ago by
Ram
43k • written 7 days ago by
atariw
▴ 10
0
votes
2
replies
268
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 7 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 7 days ago by
Fish
• 0
0
votes
0
replies
179
views
Snakemake fails to find conda in PBS
snakemake
7 days ago by
yixinzeng
• 0
0
votes
0
replies
184
views
KaryoPlot: Gene coverage over centromeric regions
Gene
coverage
Centromere
Bedtools
7 days ago by
Mary
• 0
0
votes
0
replies
172
views
Protein stability analysis
mutation
analysis
7 days ago by
marco.barr
▴ 60
1
vote
4
replies
373
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 6 days ago by
BioinfGuru
★ 1.7k • written 7 days ago by
Morteza
• 0
3
votes
1
reply
255
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 7 days ago by
Ram
43k • written 7 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
157
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
299
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 6 days ago by
ATpoint
81k • written 7 days ago by
gdfsnkfns
• 0
0
votes
4
replies
288
views
Questions about transfering wgs file to reference genome file
fasta
cram
genome
7 days ago by
me
• 0
0
votes
2
replies
251
views
WGCNA
PCA
WGCNA
EIGENGENE
7 days ago by
rajasekargutha
▴ 60
0
votes
3
replies
246
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 7 days ago by
GenoMax
141k • written 8 days ago by
neish
• 0
1
vote
0
replies
148
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 7 days ago by
Ram
43k • written 8 days ago by
ian.will
▴ 30
0
votes
0
replies
101
views
Surrogate variable analysis for paired RNA seq experiment
sva
rnaseq
ruvseq
8 days ago by
nhaus
▴ 300
1
vote
3
replies
257
views
True variants selection
vcf
bcftools
updated 7 days ago by
dthorbur
★ 1.9k • written 8 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 8 days ago by
CY
▴ 750
0
votes
0
replies
97
views
Creating a BSgenome data package from a NCBI assembly - Virus
Virus
BSgenomeForge
BSgenome
R
8 days ago by
JirMan
▴ 20
1
vote
1
reply
165
views
Failed to download data from EBI with ascp
EBI
aspera
updated 8 days ago by
GenoMax
141k • written 8 days ago by
biock
▴ 60
0
votes
0
replies
389
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
8 days ago by
Isaac
• 0
0
votes
0
replies
99
views
Combining VG graphs
vg
graphs
combine
8 days ago by
AshleeThomson
▴ 70
0
votes
0
replies
102
views
Installing SALSA and HIRise scafolding software
scafolding
SALSA
genome-assembly
HIRise
updated 7 days ago by
Ram
43k • written 8 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 8 days ago by
Pierre Lindenbaum
161k • written 8 days ago by
Saran
▴ 50
1,000 results • Page
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Installing/switching between versions of R/Rstudio/Bioconductor
How To Generate Phylogeny Tree, Based On Snps?
How To Construct Phylogenetic Tree Using Snps
Basic normalization, batch correction and visualization of RNA-seq data
A: Read counts of STAR with gff file
Comment: Free/open source 23andme-like analysis
A: How to obtain all accession.version identifiers for a BLAST database using ENTRE
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Recent Replies
Comment: Ciriquant not configuring hisat2 indexed files
by
Carlo Yague
8.6k
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
Answer: Memory usage of picard Samsort
by
tamas.malkocs
• 0
For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
Answer: Plink merge errors.
by
Dinmukhamed
• 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
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Pierre Lindenbaum
161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
b.contreras.moreira
▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
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by
Hagen
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thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
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by
Kai Xin
• 0
will look into that. Thank you very much
Comment: Korean human genome reference file
by
SeoGyun
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Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
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thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
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Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
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航太郎
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Thanks for your guide!
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