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181 results • Page
3 of 4
Sort: Rank
Rank
Views
Votes
Replies
5
votes
4
replies
635
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
3 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
91
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 4 days ago by
Ram
43k • written 4 days ago by
SHREYA
• 0
0
votes
3
replies
376
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 4 days ago by
colindaven
6.4k • written 12 days ago by
rj.rezwan
• 0
0
votes
0
replies
98
views
Merging replicates from Encode project
CHIP-seq
encode
4 days ago by
Nurken
• 0
1
vote
3
replies
226
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
4 days ago by
WouterDeCoster
47k
0
votes
3
replies
220
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 4 days ago by
mchour
• 0 • written 4 days ago by
rhossen
• 0
1
vote
1
reply
161
views
WGCNA preservation analysis
WGCNA
preservation
updated 4 days ago by
Michael
54k • written 4 days ago by
michael.flower.14
▴ 180
1
vote
3
replies
264
views
some error in building kraken2 database
metagenome
kraken2
3 days ago by
Art1ess
• 0
0
votes
1
reply
143
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 4 days ago by
bk11
★ 2.4k • written 4 days ago by
Susmita Mandal
▴ 110
0
votes
1
reply
136
views
Plots for DNA methylation data
plots
DNA
methylation
updated 4 days ago by
GenoMax
141k • written 4 days ago by
sarahawan92
▴ 10
0
votes
3
replies
494
views
python file for coding potential calculator
cpc2.py
updated 4 days ago by
atharvakarkare14
▴ 10 • written 9 days ago by
Ashok
• 0
1
vote
1
reply
170
views
Failed kmer content
kmer
illumina
ngs
updated 4 days ago by
Ram
43k • written 4 days ago by
Kasturi
• 0
0
votes
0
replies
162
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
4 days ago by
yxwucq
• 0
0
votes
0
replies
87
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 4 days ago by
Ram
43k • written 4 days ago by
SSSJec
• 0
0
votes
6
replies
320
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
4 days ago by
Sd
• 0
0
votes
2
replies
180
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
5 days ago by
sainavyav22
• 0
0
votes
1
reply
147
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 5 days ago by
Ram
43k • written 5 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
330
views
Error in cnetplot enrichplot package
R
updated 5 days ago by
Ram
43k • written 5 days ago by
Farhad
• 0
3
votes
9
replies
447
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 3 days ago by
Istvan Albert
100k • written 5 days ago by
Κοσμάς
• 0
0
votes
0
replies
110
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 5 days ago by
Ram
43k • written 5 days ago by
maxime.policarpo
▴ 200
3
votes
3
replies
200
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 5 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
c_u
▴ 520
0
votes
0
replies
93
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 5 days ago by
Ram
43k • written 5 days ago by
sansan_96
▴ 80
0
votes
0
replies
96
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 4 days ago by
Ram
43k • written 5 days ago by
Amélie
• 0
0
votes
0
replies
198
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 5 days ago by
Ram
43k • written 5 days ago by
Oak
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 5 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
3
replies
204
views
from row count to tpm
tpm
row-count
normalization
4 days ago by
michelafrancesconi9
▴ 20
1
vote
5
replies
282
views
Downsampling fastq file
downsample
fastq
updated 5 days ago by
Ram
43k • written 5 days ago by
marco.barr
▴ 80
2
votes
3
replies
328
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 1 day ago by
dsull
★ 5.9k • written 18 days ago by
javanokendo
▴ 60
0
votes
1
reply
136
views
tbtool
tbtool
updated 5 days ago by
Ram
43k • written 5 days ago by
Raman
• 0
0
votes
7
replies
317
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
GenoMax
141k • written 5 days ago by
Patadu94
• 0
3
votes
3
replies
226
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 5 days ago by
GenoMax
141k • written 5 days ago by
Mariana
▴ 10
0
votes
1
reply
128
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 5 days ago by
ATpoint
82k • written 5 days ago by
enanoide
• 0
0
votes
0
replies
88
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
5 days ago by
manaswwm
▴ 510
3
votes
3
replies
720
views
KissDE and batch effect
kissDE
kissplice
5 days ago by
david.b.rombaut
▴ 10
0
votes
0
replies
78
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
4 days ago by
alifafiq1
• 0
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
2 days ago by
Kevin Blighe
87k
0
votes
0
replies
84
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
5 days ago by
feather-W
• 0
2
votes
4
replies
279
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
3 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
85
views
Annotating single cell data automatically
cell
annotation
single
5 days ago by
Gerard
• 0
0
votes
0
replies
83
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
130
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
5 days ago by
Ben_Ensembl
★ 2.4k
2
votes
4
replies
316
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
3 days ago by
HyperEvo
• 0
0
votes
1
reply
154
views
RNA-seq bacteria contamination
RNA-seq
updated 5 days ago by
GenoMax
141k • written 5 days ago by
sh
• 0
0
votes
2
replies
194
views
Result of running of p3_in.pl
primer3
updated 5 days ago by
GenoMax
141k • written 5 days ago by
nasri
• 0
0
votes
1
reply
135
views
FAM FILE
file
Fam
5 days ago by
Eleonora
• 0
0
votes
0
replies
74
views
Imputation advice
imputation
5 days ago by
kl
▴ 10
3
votes
5
replies
275
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 5 days ago by
GenoMax
141k • written 5 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
92
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
5 days ago by
Enrique
• 0
3
votes
5
replies
554
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
5 days ago by
n_navy
• 0
0
votes
0
replies
75
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
5 days ago by
sativus
▴ 20
181 results • Page
3 of 4
Recent Votes
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
correcting for a batch in DESeq2
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Recent Replies
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
Comment: ScRNAseq-How to correctly choose cell type marker genes
by
Francesco
▴ 10
Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated
by
ATpoint
82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
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It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
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[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
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3.2k
Use the standalone version of Nextflow and specify the process-specific conda environments paths.
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22k
can you show us an exonic position in your VCF file that is all `./.`?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
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Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
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I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
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just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
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Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
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