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1,000 results • Page
5 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
96
views
Annotating single cell data automatically
cell
annotation
single
17 days ago by
Gerard
• 0
0
votes
1
reply
187
views
RNA-seq bacteria contamination
RNA-seq
updated 17 days ago by
GenoMax
142k • written 17 days ago by
sh
• 0
0
votes
0
replies
89
views
Imputation advice
imputation
18 days ago by
kl
▴ 10
0
votes
0
replies
110
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
18 days ago by
Enrique
• 0
0
votes
0
replies
86
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
18 days ago by
sativus
▴ 20
0
votes
0
replies
94
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
18 days ago by
Biostars2200
• 0
0
votes
0
replies
152
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 18 days ago by
Carlo Yague
8.7k • written 18 days ago by
Atul K.
• 0
2
votes
5
replies
515
views
Marking duplicates using UMIs
Deduplication
UMI
updated 18 days ago by
i.sudbery
19k • written 19 days ago by
Lipika
• 0
0
votes
0
replies
152
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 18 days ago by
Ram
43k • written 19 days ago by
sainavyav22
• 0
0
votes
0
replies
158
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
19 days ago by
rthapa
▴ 90
0
votes
0
replies
148
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
19 days ago by
Mamatha Y S
• 0
0
votes
2
replies
310
views
bam merging for archaic samples
samtools
bam
updated 18 days ago by
Ram
43k • written 19 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
556
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
20 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
237
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
19 days ago by
abhishekghadge
• 0
2
votes
5
replies
763
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 19 days ago by
Jesse
▴ 770 • written 20 days ago by
Ann
★ 2.4k
0
votes
0
replies
203
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 20 days ago by
Ram
43k • written 20 days ago by
mja
• 0
0
votes
0
replies
204
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
20 days ago by
Nitin
• 0
0
votes
0
replies
197
views
Chemical structure validation
structure
cap
validation
metabolite
20 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
294
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 20 days ago by
GenoMax
142k • written 20 days ago by
bioyas
▴ 10
0
votes
0
replies
223
views
Copy number variation plot
Copy-number-variation
genomics
updated 20 days ago by
Ram
43k • written 20 days ago by
Emmi
• 0
0
votes
0
replies
201
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
20 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
312
views
Could you please assist in identifying this cluster?
single-cell
updated 20 days ago by
Ram
43k • written 20 days ago by
carolofharvest
▴ 40
0
votes
0
replies
221
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 20 days ago by
Ram
43k • written 20 days ago by
Dinmukhamed
• 0
0
votes
0
replies
213
views
miRDeep2: How to get the read counts
mirdeep2
21 days ago by
Atul K.
• 0
0
votes
0
replies
217
views
Lncipedia GTF file error
Proteomics
updated 20 days ago by
Ram
43k • written 21 days ago by
atharvakarkare14
▴ 30
3
votes
3
replies
535
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 20 days ago by
swbarnes2
14k • written 21 days ago by
noodle
▴ 580
0
votes
2
replies
579
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
21 days ago by
航太郎
• 0
0
votes
0
replies
230
views
create genewise sync file in popoolation
popoolation
updated 21 days ago by
GenoMax
142k • written 21 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
411
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
21 days ago by
Ashok
• 0
0
votes
2
replies
455
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
21 days ago by
Ashok
• 0
0
votes
0
replies
229
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 21 days ago by
Ram
43k • written 21 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
460
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
20 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
222
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
17 days ago by
Javier
• 0
0
votes
0
replies
203
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
21 days ago by
enferdeflame
• 0
1
vote
1
reply
446
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 19 days ago by
Gordon Smyth
★ 7.1k • written 21 days ago by
Chris
▴ 280
0
votes
1
reply
415
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 21 days ago by
Ram
43k • written 20 months ago by
Muhammad
• 0
0
votes
0
replies
171
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 21 days ago by
Ram
43k • written 22 days ago by
bioinfo223
▴ 10
0
votes
0
replies
193
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
22 days ago by
P.
• 0
0
votes
0
replies
184
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
22 days ago by
ekirsch
• 0
1
vote
1
reply
501
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
20 days ago by
renan.igor
• 0
0
votes
0
replies
207
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
22 days ago by
synat.keam
▴ 100
0
votes
1
reply
300
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 22 days ago by
GenoMax
142k • written 22 days ago by
ycts
• 0
0
votes
4
replies
638
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
21 days ago by
Kai Xin
• 0
1
vote
1
reply
251
views
Retrieve a % coverage for each transcript
RNA-seq
updated 22 days ago by
Ram
43k • written 22 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
417
views
How can I solve this error?
metal
22 days ago by
22211020193
• 0
0
votes
0
replies
182
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 22 days ago by
GenoMax
142k • written 22 days ago by
srimmer
• 0
1
vote
2
replies
315
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 22 days ago by
Ram
43k • written 22 days ago by
aniigodwinn
• 0
0
votes
0
replies
368
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
22 days ago by
Ronin
• 0
2
votes
7
replies
927
views
Removing duplicates
duplicates
ONT
minimap2
updated 21 days ago by
noodle
▴ 580 • written 22 days ago by
quentinperriere
• 0
0
votes
1
reply
224
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 22 days ago by
DKA
▴ 40 • written 22 days ago by
james.melhorn
• 0
1,000 results • Page
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Comment: UMI-Tools knee-method has great influence on the results of white list
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I think I might know my problem. The barcodes are in this case on read2 and not on read1. Does umi-tools recognise it automatically, or do …
Comment: Microbial Signal Transduction Database
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Did you try https://mib-jouline-db.asc.ohio-state.edu/#introduction ? >The database can also be accessed via the API. The same API points …
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Anitha
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Thank you for the information.
Comment: LncRNA Nomenclature
by
jain72744
▴ 10
My data is based on gene counts and the respective gene IDs are given so I should work with ENSGs? lncRNA_transcripts <- getBM(attributes …
Answer: DESeq2 error
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At least one group needs replication. That is the short answer. For a longer answer add details on experimental design.
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82k
RNA-seq is typically analyzed on gene rather than transcript level. Are your counts gene or transcript?
Comment: EdgeR - relationship between logFC and coefficients
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gBioStar5
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Thanks a lot, this was very helpful. I'll keep that in mind.
Answer: EdgeR - relationship between logFC and coefficients
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Gordon Smyth
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Results presented by topTags() are on the log2 scale. Coefficients stored internally in the DGELRT object are on the loge scale. If you con…
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by
size_t
▴ 120
run command `explorer.exe .` in wsl terminal, and then drag file to folder
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Hi Ricardo! CAP3 is an 'older' overlap assembler from 1999 which is perfectly suited for these kinds of 'small' tasks. I used it last in my…
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That's really handy, and much more of a general solution than stripping off the directory names! So yifangt86, if you're on Linux you can …
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GenoMax
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Are you missing a `"` at the end of the URL. Doing wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
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marco.barr
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very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
Comment: Different output for read length
by
Pierre Lindenbaum
161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
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