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1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
3
votes
3
replies
503
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 12 days ago by
swbarnes2
14k • written 13 days ago by
noodle
▴ 580
0
votes
2
replies
569
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
13 days ago by
航太郎
• 0
0
votes
0
replies
225
views
create genewise sync file in popoolation
popoolation
updated 14 days ago by
GenoMax
142k • written 14 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
402
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
13 days ago by
Ashok
• 0
0
votes
2
replies
441
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
13 days ago by
Ashok
• 0
0
votes
0
replies
224
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 14 days ago by
Ram
43k • written 14 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
443
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
13 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
215
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
10 days ago by
Javier
• 0
0
votes
0
replies
192
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
14 days ago by
enferdeflame
• 0
1
vote
1
reply
434
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 11 days ago by
Gordon Smyth
★ 7.1k • written 14 days ago by
Chris
▴ 260
0
votes
1
reply
410
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 14 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
168
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 14 days ago by
Ram
43k • written 14 days ago by
bioinfo223
▴ 10
0
votes
0
replies
188
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
14 days ago by
P.
• 0
0
votes
0
replies
178
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
14 days ago by
ekirsch
• 0
1
vote
1
reply
470
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
13 days ago by
renan.igor
• 0
0
votes
0
replies
196
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
14 days ago by
synat.keam
▴ 100
0
votes
1
reply
290
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 15 days ago by
GenoMax
142k • written 15 days ago by
ycts
• 0
0
votes
4
replies
618
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
13 days ago by
Kai Xin
• 0
1
vote
1
reply
243
views
Retrieve a % coverage for each transcript
RNA-seq
updated 15 days ago by
Ram
43k • written 15 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
401
views
How can I solve this error?
metal
14 days ago by
22211020193
• 0
0
votes
0
replies
179
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 15 days ago by
GenoMax
142k • written 15 days ago by
srimmer
• 0
1
vote
2
replies
300
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 15 days ago by
Ram
43k • written 15 days ago by
aniigodwinn
• 0
0
votes
0
replies
364
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
15 days ago by
Ronin
• 0
2
votes
7
replies
891
views
Removing duplicates
duplicates
ONT
minimap2
updated 13 days ago by
noodle
▴ 580 • written 15 days ago by
quentinperriere
• 0
0
votes
1
reply
216
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 15 days ago by
DKA
▴ 40 • written 15 days ago by
james.melhorn
• 0
0
votes
1
reply
204
views
Freyja plot error
Freyja
updated 15 days ago by
Ram
43k • written 15 days ago by
Adyasha
• 0
0
votes
0
replies
168
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
15 days ago by
chemokine-1
▴ 10
0
votes
4
replies
543
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
14 days ago by
feather-W
• 0
0
votes
2
replies
265
views
Bedmethyl file format
bedmethyl
methylation
updated 15 days ago by
GenoMax
142k • written 15 days ago by
njornet
▴ 20
0
votes
0
replies
186
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
15 days ago by
Ali
• 0
2
votes
4
replies
346
views
SnpEff annotates coding duplication as intronic?
snpeff
15 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
278
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
15 days ago by
mropri
▴ 150
0
votes
0
replies
157
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
16 days ago by
shasabhi1
• 0
0
votes
0
replies
146
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
16 days ago by
Nishat
• 0
0
votes
0
replies
175
views
what exactly is a k-mer table (remora)?
remora
basecall
16 days ago by
anne
• 0
1
vote
1
reply
196
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 16 days ago by
dsull
★ 5.9k • written 16 days ago by
niruf
• 0
0
votes
0
replies
153
views
GWAS Phenotypes
GWAS
16 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
343
views
GSEA analysis in R
GSEA
R
Arabidopsis
14 days ago by
Sudip
• 0
0
votes
0
replies
129
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
16 days ago by
QX
• 0
2
votes
5
replies
517
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
15 days ago by
Bikram Kumar
• 0
0
votes
2
replies
279
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 16 days ago by
Ram
43k • written 16 days ago by
David
• 0
1
vote
2
replies
292
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
16 days ago by
bioinfo
▴ 150
0
votes
1
reply
208
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 17 days ago by
bk11
★ 2.4k • written 17 days ago by
sinhas
• 0
0
votes
1
reply
228
views
merging Seurat objects after SCT
Seurat
SCT
updated 17 days ago by
Ram
43k • written 17 days ago by
michelle.swarovski
• 0
0
votes
1
reply
238
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 17 days ago by
GenoMax
142k • written 17 days ago by
haiying.kong
▴ 360
0
votes
2
replies
292
views
RNAseq 1 control 2 different treatment
RNA-seq
16 days ago by
matteo.levorato
• 0
1
vote
0
replies
152
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 17 days ago by
Ram
43k • written 17 days ago by
Oscar
▴ 10
2
votes
0
replies
218
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
17 days ago by
Alexander
▴ 220
1
vote
2
replies
228
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 5 hours ago by
Ram
43k • written 17 days ago by
eesiribloom
▴ 80
0
votes
0
replies
146
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
17 days ago by
Balazs Horvath
▴ 10
1,000 results • Page
4 of 20
Recent Votes
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
How to convert plink data from 38th assembly to 37
How to convert plink data from 38th assembly to 37
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
Comment: Converting CRAM to FastQ
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Recent Replies
Answer: Bedtools merge minimum overlap?
by
harold.smith.tarheel
★ 4.9k
Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap?
by
bk11
★ 2.4k
Not sure if you wanting to do like this- cat your_input.bed chr1 100 200 region1 + chr1 180 300 regi…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Not every read in your data is going to match a guide. That is also true for sure. Let me clarify what I mean. For every read you should…
Answer: VG : No reference-sense paths available in the graph; falling back to generic pa
by
anovak
▴ 120
If your GFA has paths in it that are P lines with names that don't include a sample name, contig name, and separators, then those are what …
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
> if you look at a fastq file you should be able to tell for every read definitely, if it has a perfect match for a guide in it and what gu…
Answer: DiffBind: no peaks in DBA
by
jared.andrews07
★ 16k
Because `dba.analyze` is not meant to be run directly on a peaks file. Have you read the documentation? In addition, a ChIP-seq experiment…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Thank you so much! Will look it up right away.
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as yo…
Comment: Converting CRAM to FastQ
by
GenoMax
142k
Use `samtools view ` for this conversion. See discussion in https://www.biostars.org/p/9592860/ Specifically @jkbonfield's comment here --…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
No that was only from Breast cancer. You could try selecting all data and see if you are able to see all treatments in the set. No idea a…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as you …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Can you try lowering the k to k=9? Wouldn't that mess with the results since all my kmers are 20bp? > You don't have any duplicate sequ…
Comment: Provean help
by
Mensur Dlakic
★ 27k
> Else, I will happy to send over the data and kindly perform the analysis for me. This website is meant to provide advice, not service. I…
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