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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
136
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
3 days ago by
rthapa
▴ 90
0
votes
0
replies
128
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
3 days ago by
Mamatha Y S
• 0
0
votes
2
replies
245
views
bam merging for archaic samples
samtools
bam
updated 2 days ago by
Ram
43k • written 3 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
534
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
4 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
205
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
3 days ago by
abhishekghadge
• 0
2
votes
5
replies
669
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 3 days ago by
Jesse
▴ 740 • written 4 days ago by
Ann
★ 2.4k
0
votes
0
replies
182
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 4 days ago by
Ram
43k • written 4 days ago by
mja
• 0
0
votes
0
replies
185
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
4 days ago by
Nitin
• 0
0
votes
0
replies
184
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by
Ram
43k • written 4 days ago by
yifangt86
▴ 60
0
votes
0
replies
178
views
Chemical structure validation
structure
cap
validation
metabolite
4 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
255
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 4 days ago by
GenoMax
141k • written 4 days ago by
bioyas
▴ 10
0
votes
0
replies
200
views
Copy number variation plot
Copy-number-variation
genomics
updated 4 days ago by
Ram
43k • written 4 days ago by
Emmi
• 0
0
votes
0
replies
172
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
4 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
277
views
Could you please assist in identifying this cluster?
single-cell
updated 4 days ago by
Ram
43k • written 4 days ago by
Kazo
• 0
0
votes
0
replies
192
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 4 days ago by
Ram
43k • written 4 days ago by
Dinmukhamed
• 0
0
votes
0
replies
189
views
miRDeep2: How to get the read counts
mirdeep2
5 days ago by
Atul K.
• 0
0
votes
0
replies
198
views
Lncipedia GTF file error
Proteomics
updated 4 days ago by
Ram
43k • written 5 days ago by
atharvakarkare14
▴ 10
3
votes
3
replies
459
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
joe
▴ 510
0
votes
2
replies
529
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
5 days ago by
航太郎
• 0
0
votes
0
replies
208
views
create genewise sync file in popoolation
popoolation
updated 5 days ago by
GenoMax
141k • written 5 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
366
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
5 days ago by
Ashok
• 0
0
votes
2
replies
406
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
5 days ago by
Ashok
• 0
0
votes
0
replies
207
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 5 days ago by
Ram
43k • written 5 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
414
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
4 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
197
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
1 day ago by
Javier
• 0
0
votes
0
replies
172
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
5 days ago by
enferdeflame
• 0
1
vote
1
reply
405
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 3 days ago by
Gordon Smyth
★ 7.0k • written 5 days ago by
Chris
▴ 260
0
votes
1
reply
397
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 5 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
155
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 5 days ago by
Ram
43k • written 6 days ago by
bioinfo223
▴ 10
0
votes
0
replies
171
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
6 days ago by
P.
• 0
0
votes
0
replies
163
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
6 days ago by
ekirsch
• 0
1
vote
1
reply
379
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
4 days ago by
renan.igor
• 0
0
votes
0
replies
169
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
6 days ago by
synat.keam
▴ 100
0
votes
1
reply
261
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 6 days ago by
GenoMax
141k • written 6 days ago by
ycts
• 0
0
votes
4
replies
571
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
5 days ago by
Kai Xin
• 0
1
vote
1
reply
219
views
Retrieve a % coverage for each transcript
RNA-seq
updated 6 days ago by
Ram
43k • written 6 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
362
views
How can I solve this error?
metal
6 days ago by
22211020193
• 0
0
votes
0
replies
162
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 6 days ago by
GenoMax
141k • written 6 days ago by
srimmer
• 0
1
vote
2
replies
267
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 6 days ago by
Ram
43k • written 6 days ago by
aniigodwinn
• 0
0
votes
0
replies
350
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
6 days ago by
Ronin
• 0
2
votes
7
replies
800
views
Removing duplicates
duplicates
ONT
minimap2
updated 5 days ago by
joe
▴ 510 • written 7 days ago by
quentinperriere
• 0
0
votes
1
reply
192
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 6 days ago by
DKA
▴ 40 • written 7 days ago by
james.melhorn
• 0
0
votes
1
reply
180
views
Freyja plot error
Freyja
updated 6 days ago by
Ram
43k • written 7 days ago by
Adyasha
• 0
0
votes
0
replies
153
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
7 days ago by
chemokine-1
▴ 10
0
votes
4
replies
489
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
6 days ago by
feather-W
• 0
0
votes
2
replies
212
views
Bedmethyl file format
bedmethyl
methylation
updated 6 days ago by
GenoMax
141k • written 7 days ago by
njornet
▴ 20
0
votes
0
replies
166
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
7 days ago by
Ali
• 0
2
votes
4
replies
305
views
SnpEff annotates coding duplication as intronic?
snpeff
7 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
237
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
7 days ago by
mropri
▴ 150
0
votes
0
replies
140
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
7 days ago by
shasabhi1
• 0
1,000 results • Page
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Answer: To get p-values for the TPM
Comment: To get p-values for the TPM
A: Finding the centromere and telomere of cattle genome (Bos Taurus)
A: How to systematically check if a bam file is truncated
Comment: some error in building kraken2 database
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
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Comment: To get p-values for the TPM
by
ATpoint
82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
njornet
▴ 20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
Comment: Use of Kraken output for functional analysis
by
gv
• 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
Comment: To get p-values for the TPM
by
VITALA
• 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM
by
dsull
★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
dsull
★ 5.8k
I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
Comment: interpretartion of a vcf file
by
samuelkalandarov2002
▴ 10
In my case , there is only one sample : here is an example of a some variants generated using minipileup : #CHROM POS ID REF ALT QUAL FI…
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
by
b.contreras.moreira
▴ 170
This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
Comment: How to compare the quality of assemblies
by
kirillkirilenko
▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
by
Mensur Dlakic
★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
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