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515 results • Page
4 of 11
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Votes
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1
vote
1
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452
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
12 days ago by
renan.igor
• 0
0
votes
0
replies
191
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
13 days ago by
synat.keam
▴ 100
0
votes
1
reply
289
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 13 days ago by
GenoMax
141k • written 13 days ago by
ycts
• 0
0
votes
4
replies
608
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
12 days ago by
Kai Xin
• 0
1
vote
1
reply
240
views
Retrieve a % coverage for each transcript
RNA-seq
updated 13 days ago by
Ram
43k • written 14 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
397
views
How can I solve this error?
metal
13 days ago by
22211020193
• 0
0
votes
0
replies
179
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 13 days ago by
GenoMax
141k • written 14 days ago by
srimmer
• 0
1
vote
2
replies
298
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 13 days ago by
Ram
43k • written 14 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
14 days ago by
Ronin
• 0
2
votes
7
replies
881
views
Removing duplicates
duplicates
ONT
minimap2
updated 12 days ago by
noodle
▴ 580 • written 14 days ago by
quentinperriere
• 0
0
votes
1
reply
215
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 14 days ago by
DKA
▴ 40 • written 14 days ago by
james.melhorn
• 0
0
votes
1
reply
203
views
Freyja plot error
Freyja
updated 14 days ago by
Ram
43k • written 14 days ago by
Adyasha
• 0
0
votes
0
replies
168
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
14 days ago by
chemokine-1
▴ 10
0
votes
4
replies
542
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
13 days ago by
feather-W
• 0
0
votes
2
replies
258
views
Bedmethyl file format
bedmethyl
methylation
updated 14 days ago by
GenoMax
141k • written 14 days ago by
njornet
▴ 20
0
votes
0
replies
185
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
14 days ago by
Ali
• 0
2
votes
4
replies
342
views
SnpEff annotates coding duplication as intronic?
snpeff
14 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
275
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
14 days ago by
mropri
▴ 150
0
votes
0
replies
156
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
14 days ago by
shasabhi1
• 0
0
votes
0
replies
144
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
14 days ago by
Nishat
• 0
0
votes
0
replies
174
views
what exactly is a k-mer table (remora)?
remora
basecall
14 days ago by
anne
• 0
1
vote
1
reply
195
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 15 days ago by
dsull
★ 5.9k • written 15 days ago by
niruf
• 0
0
votes
0
replies
153
views
GWAS Phenotypes
GWAS
15 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
340
views
GSEA analysis in R
GSEA
R
Arabidopsis
13 days ago by
Sudip
• 0
0
votes
0
replies
129
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
15 days ago by
QX
• 0
2
votes
5
replies
510
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
14 days ago by
Bikram Kumar
• 0
0
votes
2
replies
276
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 15 days ago by
Ram
43k • written 15 days ago by
David
• 0
1
vote
2
replies
288
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
14 days ago by
bioinfo
▴ 150
0
votes
1
reply
204
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 15 days ago by
bk11
★ 2.4k • written 15 days ago by
sinhas
• 0
0
votes
1
reply
221
views
merging Seurat objects after SCT
Seurat
SCT
updated 15 days ago by
Ram
43k • written 15 days ago by
michelle.swarovski
• 0
0
votes
1
reply
227
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 16 days ago by
GenoMax
141k • written 16 days ago by
haiying.kong
▴ 360
0
votes
2
replies
285
views
RNAseq 1 control 2 different treatment
RNA-seq
15 days ago by
matteo.levorato
• 0
1
vote
0
replies
150
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 16 days ago by
Ram
43k • written 16 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
16 days ago by
Alexander
▴ 220
1
vote
1
reply
190
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 16 days ago by
GenoMax
141k • written 16 days ago by
eesiribloom
▴ 80
0
votes
0
replies
145
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
16 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
149
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
16 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
158
views
FreeBayes detection capacity
reads
freebayes
long
16 days ago by
quentinperriere
• 0
0
votes
2
replies
270
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
14 days ago by
DKA
▴ 40
0
votes
0
replies
170
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
16 days ago by
Hien
• 0
0
votes
2
replies
305
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
14 days ago by
Koketso
• 0
0
votes
0
replies
197
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 17 days ago by
Ram
43k • written 17 days ago by
menyawino
• 0
1
vote
3
replies
371
views
Ensembl gene id conversion
biomart
ensembl
updated 15 days ago by
ATpoint
82k • written 17 days ago by
naveedhasan2000
• 0
1
vote
2
replies
329
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 15 days ago by
Istvan Albert
100k • written 17 days ago by
Jiang
• 0
0
votes
0
replies
198
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
18 days ago by
YiweiZhu
▴ 30
0
votes
2
replies
328
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
17 days ago by
O.rka
▴ 710
0
votes
6
replies
573
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
16 days ago by
Dunois
★ 2.5k
4
votes
7
replies
579
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 17 days ago by
Ram
43k • written 18 days ago by
AHerik
▴ 20
0
votes
0
replies
198
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 18 days ago by
Ram
43k • written 19 days ago by
roussine
▴ 10
0
votes
0
replies
188
views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
ATAC-seq
HOMER
19 days ago by
Ronin
• 0
515 results • Page
4 of 11
Recent Votes
Comment: DESeq2 processing problems
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
Answer: Discrepancy between Log2(x) and Log2(x+1) regarding Log2FC
Answer: Verify if all the components of a pathway are present in a genomes
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▴ 200
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Recent Replies
Answer: cnetplot category names are too long
by
bkleiboeker
▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue
by
GenoMax
141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery
by
GenoMax
141k
> i keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
Comment: Telescope issue
by
eleven11
• 0
Thank you! how would I correct that?
Comment: DESeq2 processing problems
by
Ram
43k
This is an open science community, not a place to write an email to Michael Love. Please address the entire community.
Comment: Post-imputation plot
by
kl
▴ 10
All of them are G/C and A/T variants Some seem mismatches based on AF and some seem to need flipping. I guess I am confused, as in the Mich…
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
by
Nafi
• 0
Thank you for the reply I have 16 gb of RAM then I can give a try then.
Comment: Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
by
i.sudbery
19k
Can you give more details of the data you are planning to use. What is the different studies, what are the comparisons you want to make.
Comment: p-value in CIBERSORT
by
michelafrancesconi9
▴ 20
Thank you so much!!
Comment: POSSUM not working due to incompatible pssm file
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: after selecting specific GO terms to plot, cneplot is not showing any color for
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Telescope issue
by
GenoMax
141k
Looks like there is a tab missing between the sequence and the quality string.
Comment: Post-imputation plot
by
LChart
3.9k
I would pull out the variants with panel_freq ~ 1 - upload_freq and min(panel_freq, upload_freq) < 0.4. I would check if these are G/C or A…
Comment: Telescope issue
by
eleven11
• 0
Hello the output is A01940:33:GW2208142379th:3:1317:24126:3505 355 chr14 16651125 0 150M = 17034150 122900 GCTAACAGAGTTGAACCTTTCTATTG…
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
Looking at the [code here][1] `bundle_uuid` seems to be related to the submissions to HCA. Samples that ran on multiple lanes seem to have …
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