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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
80
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 1 day ago by
Ram
43k • written 1 day ago by
SHREYA
• 0
0
votes
3
replies
359
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 1 day ago by
colindaven
6.4k • written 9 days ago by
rj.rezwan
• 0
0
votes
0
replies
90
views
Merging replicates from Encode project
CHIP-seq
encode
1 day ago by
Nurken
• 0
1
vote
3
replies
188
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
0
votes
3
replies
190
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 1 day ago by
mchour
• 0 • written 1 day ago by
rhossen
• 0
1
vote
1
reply
145
views
WGCNA preservation analysis
WGCNA
preservation
updated 1 day ago by
Michael
54k • written 1 day ago by
michael.flower.14
▴ 180
1
vote
3
replies
224
views
some error in building kraken2 database
metagenome
kraken2
22 hours ago by
Art1ess
• 0
0
votes
1
reply
119
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
Susmita Mandal
▴ 110
0
votes
1
reply
120
views
Plots for DNA methylation data
plots
DNA
methylation
updated 1 day ago by
GenoMax
141k • written 1 day ago by
sarahawan92
▴ 10
0
votes
3
replies
473
views
python file for coding potential calculator
cpc2.py
updated 1 day ago by
atharvakarkare14
▴ 10 • written 6 days ago by
Ashok
• 0
1
vote
1
reply
150
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 1 day ago by
Kasturi
• 0
0
votes
1
reply
184
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 1 day ago by
Istvan Albert
100k • written 1 day ago by
qudrat.nii
▴ 10
0
votes
0
replies
154
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
1 day ago by
yxwucq
• 0
0
votes
0
replies
78
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 1 day ago by
Ram
43k • written 1 day ago by
SSSJec
• 0
0
votes
6
replies
279
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
1 day ago by
Sd
• 0
0
votes
2
replies
162
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
2 days ago by
sainavyav22
• 0
0
votes
1
reply
132
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 2 days ago by
Ram
43k • written 2 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
274
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Farhad
• 0
3
votes
9
replies
382
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 10 hours ago by
Istvan Albert
100k • written 2 days ago by
Κοσμάς
• 0
0
votes
0
replies
102
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 2 days ago by
Ram
43k • written 2 days ago by
maxime.policarpo
▴ 200
3
votes
3
replies
173
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
c_u
▴ 520
0
votes
0
replies
85
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 2 days ago by
Ram
43k • written 2 days ago by
sansan_96
▴ 80
0
votes
0
replies
90
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 1 day ago by
Ram
43k • written 2 days ago by
Amélie
• 0
0
votes
0
replies
140
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 2 days ago by
Ram
43k • written 2 days ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 2 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
3
replies
180
views
from row count to tpm
tpm
row-count
normalization
1 day ago by
michelafrancesconi9
▴ 20
1
vote
5
replies
237
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
2
votes
3
replies
303
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 2 days ago by
dsull
★ 5.8k • written 15 days ago by
javanokendo
▴ 60
0
votes
1
reply
120
views
tbtool
tbtool
updated 2 days ago by
Ram
43k • written 2 days ago by
Raman
• 0
0
votes
2
replies
176
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Patadu94
• 0
3
votes
3
replies
195
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Mariana
▴ 10
0
votes
1
reply
114
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 2 days ago by
ATpoint
82k • written 2 days ago by
enanoide
• 0
0
votes
0
replies
79
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
2 days ago by
manaswwm
▴ 490
3
votes
3
replies
709
views
KissDE and batch effect
kissDE
kissplice
2 days ago by
david.b.rombaut
▴ 10
0
votes
0
replies
70
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
1 day ago by
alifafiq1
• 0
76
votes
71
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 2 days ago by
GenoMax
141k • written 6.2 years ago by
Kevin Blighe
87k
0
votes
0
replies
78
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
2 days ago by
feather-W
• 0
2
votes
4
replies
236
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
15 hours ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
75
views
Annotating single cell data automatically
cell
annotation
single
2 days ago by
Gerard
• 0
0
votes
0
replies
76
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
118
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
2 days ago by
Ben_Ensembl
★ 2.4k
2
votes
4
replies
263
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
21 hours ago by
HyperEvo
• 0
0
votes
1
reply
139
views
RNA-seq bacteria contamination
RNA-seq
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sh
• 0
0
votes
2
replies
176
views
Result of running of p3_in.pl
primer3
updated 2 days ago by
GenoMax
141k • written 2 days ago by
nasri
• 0
0
votes
1
reply
123
views
FAM FILE
file
Fam
2 days ago by
Eleonora
• 0
0
votes
0
replies
67
views
Imputation advice
imputation
2 days ago by
kl
▴ 10
3
votes
5
replies
237
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 2 days ago by
GenoMax
141k • written 2 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
83
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
2 days ago by
Enrique
• 0
3
votes
5
replies
528
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
2 days ago by
n_navy
• 0
0
votes
0
replies
69
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
2 days ago by
sativus
▴ 20
1,000 results • Page
2 of 20
Recent Votes
Comment: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
Recent Locations •
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Popular Question
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Simone
▴ 10
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carlopecoraro2
★ 2.5k
Popular Question
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daffodil
▴ 10
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Russ
▴ 500
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pramach1
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Adyasha
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Recent Replies
Answer: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
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