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121,199 results • Page
9 of 2424
Sort: Rank
Rank
Views
Votes
Replies
1
vote
1
reply
348
views
Tools for clustering genes rather than samples for bulk RNA-seq
time
Bulk
RNA-seq
course
clustering
updated 6 weeks ago by
i.sudbery
21k • written 6 weeks ago by
ATS
• 0
2
votes
2
replies
498
views
what database should I use for de novo genome in AUGUSTUS
genome
AUGUSTUS
galaxy
annotation
updated 6 weeks ago by
lieven.sterck
15k • written 7 weeks ago by
Jl
• 0
1
vote
8
replies
701
views
Is there a tool to obtain GO terms for thousands of genes at once?
permutations
Genes
updated 25 days ago by
GenoMax
151k • written 6 weeks ago by
Ana
▴ 10
0
votes
1
reply
301
views
cant make the correct matrix
logfc
csv
updated 6 weeks ago by
lieven.sterck
15k • written 6 weeks ago by
Naila
• 0
1
vote
4
replies
489
views
FIxing Gene Models in Funannotate
genomics
funannotate
fungus
annotation
6 weeks ago by
SomeOne
▴ 170
1
vote
7
replies
608
views
How to Make Cell Order identical Between Two Seurat Objects in R?
R
seurat
scRNA-seq
updated 6 weeks ago by
yura.grabovska
▴ 770 • written 7 weeks ago by
zhang616123
• 0
0
votes
3
replies
421
views
Assign different color in same section of Chord diagram in R
Chart
R
Diagram
Plot
Chord
updated 6 weeks ago by
Bastien Hervé
6.3k • written 7 weeks ago by
Jonathan Yoou
▴ 70
0
votes
0
replies
267
views
News:
Live Online course: Introduction to Python, April, 2025
python
programming
course
7 weeks ago by
soledad.esteban
• 0
1
vote
4
replies
434
views
Niormalization process in creating heatmap
Z
heatmap
score
Normalization
updated 7 weeks ago by
ATpoint
88k • written 7 weeks ago by
ZuelTech
• 0
1
vote
14
replies
1.0k
views
Lacking exons in gtf file of a virus' genome
gtf
exon
Mapping
Hazara
VirusGenome
updated 7 weeks ago by
colindaven
7.4k • written 7 weeks ago by
ZuelTech
• 0
1
vote
4
replies
2.1k
views
Should I process two complete sets of 10x single-cell multiomics sequencing files from one donor together or separately?
10x_multiome
ENCODE
cellranger_arc
updated 7 weeks ago by
swbarnes2
14k • written 7 weeks ago by
Wu-Sheng Zhang
• 0
1
vote
4
replies
476
views
Count matrices plotting
count
matrix
scanpy
7 weeks ago by
NIkita
• 0
3
votes
8
replies
631
views
Filter snRNA-seq .fastq files based on barcodes
snRNA-seq
scRNA-seq
FASTQ
bbmap
updated 6 weeks ago by
GenoMax
151k • written 7 weeks ago by
connorjfausto
▴ 30
0
votes
1
reply
301
views
Defining Sex Chromosomes in PLINK for a Camel Genome
plink
vcf
updated 7 weeks ago by
chrchang523
11k • written 7 weeks ago by
Smilesky
• 0
0
votes
0
replies
183
views
Why is the IC50 of the low-risk group always lower than that of the high-risk group?
OncoPredict
7 weeks ago by
nuorain
▴ 40
0
votes
0
replies
211
views
News:
Introduction to Epigenomics course
Epigenomics
RNA-seq
ATAC-seq
Chip-seq
HI-C
7 weeks ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
338
views
Remove batch effect RnaSeq (RUVg)
ruvg
batch
rnaseq
remove
7 weeks ago by
aLex97
• 0
0
votes
0
replies
201
views
Annotation of CpG, DMRs and DMPs with MethylKit and Genomation in R
dmp
methylkit
dmr
CpG
7 weeks ago by
egascon
▴ 60
1
vote
0
replies
293
views
Tool:
A rust binding for pairwise/multiple sequence aligner: bsalign-rs
bsalign
alignment
6 weeks ago by
dwpeng
▴ 120
0
votes
2
replies
434
views
Perform DEGs with pyDESeq2 in CCLE Melanoma Data But Contains Negative Values
DEG
CCLE
Melanoma
pyDESeq2
7 weeks ago by
mete.han.celebi
• 0
0
votes
0
replies
255
views
energy minimisation
Energy
updated 7 weeks ago by
Pierre Lindenbaum
166k • written 7 weeks ago by
swarnadurga66666m
• 0
0
votes
1
reply
316
views
How to concatenate different domains in the target database identified by hmmsearch
multiple
domains
hmmsearch
updated 7 weeks ago by
GenoMax
151k • written 7 weeks ago by
Yongjie Zhang
▴ 110
0
votes
1
reply
322
views
How to filter Hmmsearch alignment
Hmmsearch
updated 7 weeks ago by
Mensur Dlakic
★ 29k • written 7 weeks ago by
Yongjie Zhang
▴ 110
2
votes
3
replies
2.6k
views
Defining residues as buried or exposed based in ASAs/RSAs
structural-bioinformatics
protein-biology
updated 7 weeks ago by
Dan A
• 0 • written 3.8 years ago by
Agenor Neto
▴ 10
1
vote
1
reply
380
views
Understanding Re-use of Query Sequences in Long Read Alignments
Alignment
PacBio
pbmm2
Minimap2
updated 7 weeks ago by
LauferVA
4.7k • written 7 weeks ago by
Charles-Alexandre Roy
▴ 50
0
votes
2
replies
499
views
Discrepancy between BAM and vcf
discrepancy
vcf
DRAGEN
updated 7 weeks ago by
Istvan Albert
102k • written 7 weeks ago by
louis-gil
• 0
2
votes
1
reply
608
views
Question about `vg giraffe`
vg
updated 7 weeks ago by
GenoMax
151k • written 7 weeks ago by
zhengluo
• 0
1
vote
2
replies
671
views
Difference in mapping rate when aligned with mapper.pl of miReep2 and bowtie1
small-RNASeq
miRNASeq
bowtie
miRDeep2
updated 19 hours ago by
LINHUI
• 0 • written 11 months ago by
MIKA
• 0
3
votes
3
replies
613
views
How to align library of highly similar sequences
MPRA
variant
alignment
BWA
SNV
7 weeks ago by
rustyshackleford
• 0
0
votes
3
replies
1.9k
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 7 weeks ago by
Bastien Hervé
6.3k • written 24 months ago by
Sun
• 0
0
votes
1
reply
360
views
Reannotation of complete bacterial genome sequence
re-annotation
genome
whole
Automated
updated 7 weeks ago by
Juke34
9.2k • written 7 weeks ago by
csag6433
• 0
0
votes
2
replies
970
views
What are the best tools for quantifying allele-specific expression from bulk RNA-seq data these days?
ase
phASER
allele
gene
gatk
updated 7 weeks ago by
GenoMax
151k • written 7 weeks ago by
Paulo
▴ 10
4
votes
4
replies
3.7k
views
Lift over of GWAS summary stat file from Hg38 to Hg19
Hg38
linux
Liftover
GWAS
Hg19
updated 7 weeks ago by
Mllepnos
• 0 • written 3.9 years ago by
AVA
▴ 40
8
votes
3
replies
581
views
How do I install Terminal on Windows?
Terminal
updated 7 weeks ago by
5heikki
11k • written 7 weeks ago by
phyms
• 0
1
vote
1
reply
360
views
Mapping reversion mutations
NGS
reversion
mutation
updated 7 weeks ago by
Ram
45k • written 7 weeks ago by
reddyraghuveer664
• 0
0
votes
0
replies
287
views
Issue with Fetching Population Allele Frequency in gnomAD GraphQL API
allelle
frequency
api
GraphQL
gnomad
7 weeks ago by
DareDevil
★ 4.4k
0
votes
1
reply
369
views
Attempts to demultiplex long reads from .pod5 result in unclassified reads
dorado
sequencing
Long-read
demultiplex
updated 7 weeks ago by
GenoMax
151k • written 7 weeks ago by
Placeholder@12654926
• 0
0
votes
1
reply
369
views
Issue with BSgenomeForge::forgeBSgenomeDataPkgFromNCBI
R
BSgenomeForge
BSgenome
NCBI
updated 7 weeks ago by
ATpoint
88k • written 7 weeks ago by
noodle
▴ 650
1
vote
1
reply
371
views
Batch effect or biological difference
Batch-effect
updated 7 weeks ago by
Ram
45k • written 7 weeks ago by
cynthier
• 0
3
votes
2
replies
449
views
Inconsistency between VCF and HGVS
VEP
7 weeks ago by
Senanu
▴ 30
0
votes
1
reply
328
views
VCFtools + easySFS snp # discordance
RADtags
vcftools
updated 6 weeks ago by
Istvan Albert
102k • written 7 weeks ago by
laurasachica7
• 0
0
votes
4
replies
3.3k
views
Generating Multiple Alignment Format file (Maf)
maf
multiple-alignment
mafft
updated 7 weeks ago by
Ram
45k • written 8.5 years ago by
roz_safavi
• 0
3
votes
6
replies
677
views
STAR: Paired alignment gets ~18% unmapped (too short), but single reads get >90% mapping
paired-end
star
rnaseq
7 weeks ago by
Davor
• 0
1
vote
0
replies
498
views
Job:
bioinformatician position, Ohio State University, Columbus, USA
bioinformatician
updated 7 weeks ago by
GenoMax
151k • written 7 weeks ago by
ilaria.palmisano
▴ 10
3
votes
4
replies
525
views
Coverage drop at assembly ends
bowtie2
bw-mem
alignment
minimap2
updated 7 weeks ago by
GenoMax
151k • written 7 weeks ago by
alenew.am
▴ 10
4
votes
7
replies
803
views
How to identify additional SNPs on EPICv2
SNPs
methylation
EPIC
updated 6 weeks ago by
Papyrus
★ 3.1k • written 8 weeks ago by
Basti
★ 2.1k
0
votes
1
reply
385
views
jcvi:ValueError: A total of 0 anchor was found. Aborted.
jcvi
Collinearity
updated 7 weeks ago by
Ram
45k • written 7 weeks ago by
JieQY
• 0
0
votes
5
replies
730
views
SNPcheck alternative
SNPCheck
updated 7 weeks ago by
GenoMax
151k • written 7 weeks ago by
KirGen
▴ 30
0
votes
0
replies
274
views
Comparing HMMER vs. HHrepID for LRR Repeat Detection and Boundary Consistency
hmmer
repeats
7 weeks ago by
jllPons
• 0
0
votes
0
replies
314
views
circos plot help
visualization
SNV
genomics
circos
updated 7 weeks ago by
Ram
45k • written 7 weeks ago by
Genomancer
• 0
121,199 results • Page
9 of 2424
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Answer: How common is it to split fastq files prior to bwa mem to increase parallelizati
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Comment: Drastic drop in RNA-seq read mapping rate when disabling gaps in Bowtie2
by
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151k
What is the reason for now allowing gaps? Generally one would not want gaps when aligning microRNA or small RNA data but not regular RNA.
Comment: SSL and Syntax Errors when using fasterq-dump (SRA Toolkit)
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151k
In a case like this it may be best to directly work with EVA help desk since they can see your submission and should be able to guide you t…
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151k
> I don't encounter any errors during genome indexing or mapping Can you show us a listing of the index files (along with their sizes) th…
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88k
In the log I only see logs of the genome indexing process, not of the actual alignment. You also seem to do GTF-guided alignment, but this …
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The objective was to develop an algorithm for PRS calculation based on a given sample's SNP data. I chose to test their risk for type 2 dia…
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**Here is the code that I have used to generate the indexed genome** STAR --runThreadN 10 --runMode genomeGenerate --genomeDir ./ --ge…
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21k
The mouse genome is only about 2% coding exons. 98% of the genome is sequence that is not present in a mature mRNA transcript. Most of your…
Comment: Fold change - a final explanation
by
i.sudbery
21k
This is a new question. Please create a new post.
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1769mkc
★ 1.3k
add the source so in future people can use that
Comment: STAR aligner problem on local laptop
by
Bastien Hervé
6.3k
The STAR command line you are running is needed to help you here. Please add it to your post.
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Please show a command line and log output. 40GB is ok probably, depending on settings.
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Where this noFeature reads can align to then? How to assess the quality> yes the method for library prep itself included rRNA depletion...R…
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Ah yes good point, agreed.
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I tried with 2 paired-end BAM files from different GSE IDs. One of them gave 35149287 fc0 reads, 18809574 fc1 reads and 18645129 fc2 reads.…
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