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122,232 results • Page
19 of 2445
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0
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412
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How do I figure out which chain a ligand is bound to using rcsb-api?
rcsb
updated 5 months ago by
GenoMax
154k • written 5 months ago by
Priyal
▴ 10
1
vote
2
replies
691
views
Deseq2
PyDeseq2
Deseq2
updated 5 months ago by
GenoMax
154k • written 5 months ago by
sk_24
▴ 10
0
votes
0
replies
830
views
News:
In-Person NGS Epigenomics Workshop (November 3-5 in Munich, Germany)
ChIPSeq
BisulfiteSeq
ATACSeq
workshop
5 months ago by
ecSeq Bioinformatics
▴ 20
1
vote
0
replies
807
views
News:
Announcing a New Journal – Bioinformatics Methods and Applications – Now Open for Submissions
bioinformatics
5 months ago by
Wei
▴ 10
2
votes
1
reply
649
views
How to address conflicting circRNA expression results between public datasets and published studies? is it normal?
CicRNA-GEO
updated 5 months ago by
rfran010
★ 1.7k • written 5 months ago by
ParastooA
▴ 20
1
vote
6
replies
891
views
Help for Pooled Exome Sequencing SNP Analysis
GATK
SNP
Exome
polymorphisms
5 months ago by
alejandro.mejiam1
▴ 20
0
votes
0
replies
422
views
low variant sites similarity between linear reference and vg call path
call
vg
updated 5 months ago by
GenoMax
154k • written 5 months ago by
PolenP
▴ 10
0
votes
0
replies
552
views
KEGG pathways. How to plot the log2FC of genes collapsed into a "node"?
visualization
DEG
KEGG
R
pathway
5 months ago by
txema.heredia
▴ 280
0
votes
5
replies
959
views
MACS3 Parameter adjustments
human
libraries
illumina
callpeak
macs3
5 months ago by
María José
▴ 10
4
votes
1
reply
950
views
DeSeq2 how to change design matrix when samples are exclusive: error in “Model matrix not full rank” checkFullRank(full)
Deseq2
updated 5 months ago by
ATpoint
90k • written 5 months ago by
totoroGirl
• 0
0
votes
1
reply
608
views
Interactive UMAP scanpy
UMAP
scanpy
interactive
updated 5 months ago by
antonioggsousa
3.4k • written 5 months ago by
npont
▴ 20
9
votes
5
replies
1.3k
views
Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq with limma-voom?
Batchcorrection
VOOM
DEGanalysis
Limma
bulkRNA
updated 5 months ago by
i.sudbery
22k • written 5 months ago by
Sumeet
▴ 10
8
votes
5
replies
961
views
Log2FC track Visualization in IGV
visualization
IGV
RNASeq
5 months ago by
SomeOne
▴ 260
0
votes
0
replies
697
views
News:
online course: Sex Chromosome Evolution - 6–10 October 2025
SexChromosome
Evolution
Genomics
5 months ago by
Physalia-courses
★ 2.7k
0
votes
0
replies
394
views
GSEA of sugarcane
GSEA
5 months ago by
analyst
▴ 70
4
votes
6
replies
1.4k
views
DESeq2 design for differential expression with 2 timepoints and 2 controls
Transcriptomic
Feeding
DESeq2
RNAseq
updated 5 months ago by
txema.heredia
▴ 280 • written 5 months ago by
Cristina
• 0
1
vote
12
replies
1.4k
views
FeatureCount : Successfully assigned alignments is low
rnaseq
featurecount
5 months ago by
HarperReed
▴ 10
1
vote
2
replies
633
views
Difficulties in calling peaks for CUT&RUN (IgG control with high RPKM value)
CUTRUN
calling
IgG
peak
5 months ago by
Basti
★ 2.1k
7
votes
3
replies
1.0k
views
custom BED to UCSC genome browser
browser
ucsc
ucsc-genome-browser
genome
methylation
bed
5 months ago by
npont
▴ 20
1
vote
2
replies
636
views
unmatched number of reads after trimming treatment by afterqc
NGS
genome
assembly
5 months ago by
德水
• 0
0
votes
1
reply
597
views
Extract Specific RNA-seq reads from BAM using deeptools
RNA-seq
deeptools
updated 5 months ago by
GenoMax
154k • written 5 months ago by
Qilin
• 0
0
votes
11
replies
1.4k
views
Error Correction with Tadpole and BBMerge
BBmerge
tadpole
error
correction
5 months ago by
Jon
• 0
2
votes
1
reply
523
views
Quantification for small RNAseq data
quantification
seq
data
smallRNA
updated 5 months ago by
rfran010
★ 1.7k • written 5 months ago by
ZuelTech
• 0
9
votes
4
replies
1.7k
views
GrCh37 or GrCh38? That is the question.
GrCh37
sequence
human
genome
GrCh38
5 months ago by
Anjan
▴ 850
0
votes
2
replies
807
views
Scvi - Integration
integration
singlecell
scvi
5 months ago by
t.fosk
• 0
7
votes
3
replies
747
views
Bootstrapping in RNA-seq
bootstrapping
RNAseq
updated 5 months ago by
rfran010
★ 1.7k • written 5 months ago by
littlebioinformatician
• 0
1
vote
2
replies
757
views
Computing ka/ks ratio for individual genes.
ks
ka
evolution
selection
5 months ago by
Shakunthala Natarajan
▴ 10
1
vote
0
replies
1.7k
views
Job:
Several Permanent Positions as Bioinformatician/Computational Biologist/System Developer/Project Leader at Swedish national research infrastructures
Sweden
SciLifeLab
Genomics
Uppsala
Proteomics
5 months ago by
Matthias Zepper
5.2k
2
votes
2
replies
614
views
Obtaining a BED/GTF from Ensembl
rna-seq
ensembl
bcftools
rna
5 months ago by
joe_genome
▴ 70
0
votes
0
replies
708
views
News:
New Bioconductor and Physalia Collaboration!
Bioconductor
DataAnalysis
Genomics
5 months ago by
Physalia-courses
★ 2.7k
1
vote
1
reply
612
views
Read1 and read2 asymmetry in stranded, paired-end rnaseq data aligned by STAR
stranded
STAR
RNAseq
antisense
sense
updated 5 months ago by
rfran010
★ 1.7k • written 5 months ago by
yampolsk
▴ 10
0
votes
1
reply
819
views
Does the order of SplitNCigarReads and MarkDuplicates affect RNA-seq variant calling results?
variantcalling.
rnaseq
gatk
updated 5 months ago by
rfran010
★ 1.7k • written 5 months ago by
iamsmor
• 0
0
votes
0
replies
413
views
Should I standardize age and age2 as covariates in GWAS models?
GWAS
covariates
5 months ago by
yu
• 0
5
votes
6
replies
1.0k
views
Venn Diagram
VennDiagram
updated 5 months ago by
lieven.sterck
16k • written 5 months ago by
Nasim Gandomdoust
• 0
0
votes
1
reply
491
views
PhageTerm error
phage
genome
phageterm
assamble
updated 5 months ago by
GenoMax
154k • written 5 months ago by
NIkita
• 0
0
votes
1
reply
488
views
WGCNA Workflow from GEO FASTQ Files – Expression Type, Sample Inclusion, and Preprocessing
fastq
wgcna
rna
updated 5 months ago by
GenoMax
154k • written 5 months ago by
tutorwhizzz
• 0
0
votes
0
replies
387
views
small RNA-Seq pipeline Standstill
NGS
miRNA
5 months ago by
anthony.santana.703.j
▴ 30
2
votes
3
replies
634
views
comparison interpretation
model-matrix
contrast
design-matrix
4 months ago by
jkim
▴ 230
0
votes
0
replies
366
views
piRNAs Analysis Pipelines
piRNAs
smallRNA
5 months ago by
GA
• 0
1
vote
1
reply
643
views
Beagle PATH (partially) recognised on Ubuntu 22.04
Ubuntu
Beagle
Beast
MCMC
updated 5 months ago by
GenoMax
154k • written 5 months ago by
Luca Arbore
▴ 10
0
votes
0
replies
381
views
CNV Computation with HoneyBadger
CNV
HoneyBADGER
updated 5 months ago by
GenoMax
154k • written 5 months ago by
mete.han.celebi
• 0
0
votes
0
replies
449
views
How to predict programatically TFBS and calculate PWM Score as JASPAR
PWMScan
TFBS
JASPAR
5 months ago by
t.kajiyama
• 0
0
votes
14
replies
1.5k
views
Host Removal Issues Human/Dog with samples containing Eukaryotic species
Mapping
Eukarotic
Host
updated 4 months ago by
Ram
45k • written 5 months ago by
Jon
• 0
1
vote
1
reply
773
views
Pharokka Error
error
annotating
viral
pharokka
genome
updated 5 months ago by
Mensur Dlakic
★ 30k • written 5 months ago by
NIkita
• 0
0
votes
0
replies
417
views
Combining Metatranscriptomics (Mtx) and Metagenomics (Mgx)
metagenomics
reference-based
Metatranscriptomics
alignment
updated 5 months ago by
GenoMax
154k • written 5 months ago by
rk009
• 0
1
vote
1
reply
454
views
how to make a circular plot of variants
circular
plot
updated 5 months ago by
Pierre Lindenbaum
166k • written 5 months ago by
analyst
▴ 70
2
votes
6
replies
895
views
GSEA analysis
RNA-seq
RNA
analysis
updated 5 months ago by
GenoMax
154k • written 5 months ago by
Ahmed
• 0
0
votes
1
reply
505
views
how to make go term plot and kegg pathway plot using InterProScan output
interproscan
4 months ago by
analyst
▴ 70
1
vote
3
replies
987
views
Why little difference in RNAseq alignment when flipping forward and reverse strand with paired end reads
mRNA
rna-seq
bowtie
alignment
updated 5 months ago by
swbarnes2
15k • written 5 months ago by
JourneyToAbyss
▴ 250
0
votes
1
reply
514
views
Questions about sample_accession_id and file_accession_id from EGA files
EGA
open
WGS
data
updated 5 months ago by
GenoMax
154k • written 5 months ago by
askif4
▴ 20
122,232 results • Page
19 of 2445
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Comment: "sortmerna" quitting early--is this is a memory issue?
by
Andrew
• 0
Ok, here's the output: https://pastebin.com/uEHSckHS This run had the working directory in the default location, in sortmerna\run, but it …
Answer: Problems in Molecular Docking in Autodock vina
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Anonsirs
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Try to re run the command by first starting meeko and rdkit . to convert PDB files to PDQT files. It can help vina recognize the atom . a…
Comment: "sortmerna" quitting early--is this is a memory issue?
by
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• 0
Do you mean the maximum % RAM usage it reaches right before the moment it quits? As I said, the computer has 16 GB RAM, and the run fails w…
Comment: Chip-seq analysis Diffbind
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Thank you very much for always answering my doubts and questions. I truly value and appreciate it because it helps me understand the result…
Comment: Minimap2 segfaults when mapping Nanopore reads to a very large reference databas
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firefox91
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Many thanks !
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154k
> I have access to both the raw reads and the previously assembled transcriptome submitted to TSA. and > I am trying to determine wheth…
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly
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★ 3.2k
There are a few factors to consider: **The quality of the existing reference.** If there is a high quality chromosome level assembly,…
Comment: "sortmerna" quitting early--is this is a memory issue?
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8.1k
Pls add the output and your system (especially RAM), no one here can guess.
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There are software packages for power analysis such as https://academic.oup.com/bioinformaticsadvances/article/5/1/vbaf150/8173951.
Comment: Data integration single cell using Harmony
by
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3.5k
Run QC for each sample separately, then merge run SCTransform, PCA, then Harmony, UMAP, FindNeighbors and FindClusters.
Comment: Data integration single cell using Harmony
by
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Thank you for the quick answer. I still have a doubt. It would be better to pre-process each sample separately (*filtering, SCTransform…
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I checked the memory before executing this command. I made a bash script on Ubuntu to run it on 15 folders. But, this problem happened in f…
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Many proteins have multiple domains, and are correctly classified with multiple KO numbers. That's not a bug in `kofam_scan` but rather a r…
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If you want to visualise the mapping; take a look at using IGV. It just requires the genome you used to map the reads and the BAM output (n…
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shevch2009
▴ 20
Thanks, I had completely forgotten that METABOLIC works with protein sequences. That will work :) I was just trying to figure out how peop…
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