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120,839 results • Page
2 of 2417
Sort: Rank
Rank
Views
Votes
Replies
0
votes
3
replies
255
views
Normalize RNAseq data on RT-dPCR or RT-qPCR
RNAseq
updated 4 days ago by
ATpoint
87k • written 4 days ago by
lagartija
▴ 160
0
votes
2
replies
255
views
Is there a way to import a large amount of regions of interest into IGV
sequencing
igv
genomics
ngs
updated 4 days ago by
GenoMax
150k • written 4 days ago by
Mark
▴ 30
4
votes
10
replies
668
views
Question about an alignment
ces
sequencing
alignment
3 days ago by
barslmn
★ 2.4k
0
votes
2
replies
257
views
Arioc (read mapping) ref sequence length error
mapping
gpu
arioc
read
4 days ago by
Michael
• 0
0
votes
0
replies
303
views
When I want to compare two groups at multiple time points in scRNA-seq datasets, the criteria for the genes to be analyzed
Seurat
scRNA-seq
4 days ago by
Apprentice
▴ 170
7
votes
6
replies
558
views
Heatmap problem in R
R
Heatmap
5 days ago by
ParastooA
▴ 20
3
votes
4
replies
392
views
Bacterial VCF file annotation using snpEff error
SnpEff
5 days ago by
1769mkc
★ 1.2k
1
vote
4
replies
365
views
Coverage depth using samtools
samtools
ngs
depth
sequencing
coverage
4 days ago by
slzr_
• 0
4
votes
4
replies
375
views
MarkDuplicates RNASeq: A few samples look weird. What could be the cause?
qc
markduplicates
picard
rnaseq
updated 6 days ago by
GenoMax
150k • written 6 days ago by
Davor
• 0
0
votes
2
replies
294
views
Data Integrity (NCBI SRA and TCGA)
clinic
metadata
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 6 days ago by
umarfaruksahin
• 0
0
votes
0
replies
1.3k
views
concatenating 2 differently-imputed VCF files then filtering by imputation score to keep the higher imputation score imputed vaiant from duplicate v…
Imputation
filtration
score
duplicate
variants
6 days ago by
SalmaElShafie
• 0
0
votes
0
replies
192
views
loss of coverage using gargammel
gargammel.pl
ART
AdapterRemoval
6 days ago by
anna.utili
• 0
1
vote
2
replies
309
views
What is the stance on optical duplicates in RNASeq?
duplicates
rnaseq
optical-duplicates
2 days ago by
Davor
• 0
2
votes
4
replies
416
views
How to rank genes for GSEA using edgeR-LRT results ?
DEG
edgeR
updated 4 days ago by
dariober
15k • written 7 days ago by
Picasa
▴ 660
4
votes
3
replies
435
views
Using bulk RNA-seq DE results to perform PCA in single cell RNA-seq
Single-cell
scRNAseq
updated 4 days ago by
jared.andrews07
★ 18k • written 8 days ago by
Oli
• 0
3
votes
1
reply
260
views
Access to dbSnp137 (GRCh37)
dbSnp137
GRCh38
dbSnp
updated 6 days ago by
Marcellie87
▴ 10 • written 6 days ago by
Steven
▴ 50
0
votes
0
replies
186
views
How to convert RAP-DB/MSU IDS to RefSeq/Entrez Gene IDS?
IRGSP
Entrez
RAP-DB
RefSeq
6 days ago by
ChanderKant (CK) Chaudhary
▴ 10
4
votes
4
replies
1.8k
views
Annotating single cell data automatically
single-cell
updated 6 days ago by
S.Ghazala
▴ 60 • written 11 months ago by
Gerard
▴ 10
4
votes
0
replies
268
views
News:
Join the online/distributed nf-core Hackathon next week!
nf-core
nextflow
container
workflows
bioinformatics
7 days ago by
Matthias Zepper
5.1k
0
votes
3
replies
343
views
Non variants sites of the genome (gVCF file)
non
genome
variants
sites
gVCF
updated 3 days ago by
LauferVA
4.6k • written 7 days ago by
heureuse
▴ 10
1
vote
1
reply
258
views
Choosing the "right" sequence as an input control
input
control
chipseq
updated 7 days ago by
ATpoint
87k • written 7 days ago by
mark.pekarsky
▴ 20
1
vote
2
replies
312
views
Unable to parse config file
nextflow
nf-core
Pulled
form
github
updated 6 days ago by
Phil Ewels
★ 1.4k • written 7 days ago by
JieQY
• 0
0
votes
1
reply
219
views
Seeking Guidance on Selecting Control ChIP Sequences for nf-core/chipseq Pipeline
SRR
nf-core
chipseq
updated 9 hours ago by
mark.ziemann
★ 2.0k • written 7 days ago by
mark.pekarsky
▴ 20
0
votes
0
replies
180
views
Problem with GSVA output
GSVA
RNAseq
7 days ago by
a.stef.44
▴ 10
0
votes
2
replies
269
views
Using UMI-tools on Smart-seq3 RNA-Seq data
rna-seq
UMI
UMI-tools
smart-seq3
updated 7 days ago by
Ram
45k • written 7 days ago by
Agastya
▴ 10
1
vote
5
replies
428
views
Remove site with only missing data
Fasta
updated 7 days ago by
Pierre Lindenbaum
165k • written 8 days ago by
Leane
• 0
0
votes
3
replies
318
views
Problems with Seaborn plots in Python
python
sns
plot
updated 7 days ago by
Wayne
★ 2.1k • written 7 days ago by
egascon
▴ 60
4
votes
4
replies
456
views
Downloading full list of Homo sapiens genes
Genes
7 days ago by
nigussie.amu
• 0
0
votes
1
reply
256
views
How to normalise Nanopore mRNA sequencing data between two cell lines
Nanopore
RNAseq
Normalization
updated 4 days ago by
lagartija
▴ 160 • written 7 days ago by
Mo
▴ 50
2
votes
5
replies
4.3k
views
Python library for parsing bcftools stats file
bcftools
updated 8 days ago by
Pierre Lindenbaum
165k • written 7.7 years ago by
William
★ 5.3k
0
votes
0
replies
198
views
Manta SV (specially Translocation)
manta
Structural-Variant
updated 7 days ago by
Ram
45k • written 8 days ago by
Nai
▴ 50
0
votes
3
replies
491
views
Cytoscape COLOUR EDGES
Reulatory
Cytoscape
Networks
updated 8 days ago by
Scooter
▴ 290 • written 16 days ago by
SKY
▴ 60
3
votes
3
replies
1.2k
views
How to perform PPI network analysis in STRING for newly sequenced bacterial genome ?
Proteomics
cytoscape
network
STRING
updated 3 days ago by
bioinfo_enthusiast
• 0 • written 3.8 years ago by
Kumar
▴ 120
0
votes
0
replies
206
views
How to perform burden test using plink /seq
plink-seq
Burden-Test
updated 7 days ago by
Ram
45k • written 8 days ago by
aiswaryabioinfo
▴ 30
0
votes
3
replies
290
views
Higher number of reads mapped to transcriptome vs genome in star mapping
riboseq
star
bam
transcriptome
alignment
updated 8 days ago by
i.sudbery
21k • written 8 days ago by
paguirreazorin
• 0
1
vote
4
replies
461
views
Visualisation of read depth
coverage
read-depth
variant-calling
updated 7 days ago by
Ram
45k • written 8 days ago by
AIMAR
• 0
7
votes
5
replies
795
views
Tool:
AliNe (Alignment in Nextflow)
nextflow
alignment
8 days ago by
Juke34
9.2k
0
votes
0
replies
222
views
construct PKN
REGULATORY
PKN
MOUSE
NETWORKS
GENE
8 days ago by
rahma.khoualdia
• 0
3
votes
5
replies
447
views
Tool for automatic immune cell annotation in MOUSE?
immune
single-cell
annotation
3 days ago by
txema.heredia
▴ 210
4
votes
12
replies
7.1k
views
12 follow
How to draw venn diagram for two CNV lists?
venn
updated 8 days ago by
5heikki
11k • written 10.3 years ago by
lyz10302012
▴ 480
0
votes
2
replies
275
views
merging diploid and tetraploid vcfs
bcftools
diploid
tetraploid
8 days ago by
analyst
▴ 60
0
votes
1
reply
241
views
TMM normalized CPM
TPM
CPM
TMM
updated 7 days ago by
ATpoint
87k • written 8 days ago by
maryak
▴ 20
0
votes
0
replies
177
views
Normlizatiom in DiffBind
DiffBind
CHIP-Seq
8 days ago by
Siqi
• 0
0
votes
1
reply
232
views
Obtain genome coordinates for a DNA sequence using ENSEMBL API
Ensembl
API
updated 8 days ago by
GenoMax
150k • written 8 days ago by
Ishan
• 0
0
votes
0
replies
190
views
Forum:
Decoding Corvid Intelligence: Genomics, AI & the Genetics of Cognition
neurogenetics
comparative-genomics
bioinformatics
genomics
machine-learning
updated 8 days ago by
Ram
45k • written 8 days ago by
EvoGenExplorer
• 0
3
votes
5
replies
465
views
GBWT Construction Error: "Sources X and Y both have node Z" When Building GBZ from GFA
vg
updated 5 days ago by
Jouni Sirén
▴ 610 • written 9 days ago by
Sauers
▴ 20
8
votes
16
replies
743
views
6 follow
prokka with too many "hypothetical proteins" and genome comparison
comparison
genome
galaxy
prokka
8 days ago by
avinci1
▴ 20
0
votes
1
reply
265
views
Split paired ended hWGS FASTq files to simulate difference sequence coverage
whole-genome-sequencing
wgs
FASTQ
coverage
updated 9 days ago by
shelkmike
★ 1.5k • written 9 days ago by
DJBill
▴ 20
1
vote
11
replies
625
views
OMA use case
oma
omastandalone
updated 3 days ago by
GenoMax
150k • written 10 days ago by
nmalexan
• 0
0
votes
0
replies
189
views
News:
Machine Learning for Longitudinal Data with Python – Online Course (6-9 May)
MachineLearning
LongitudinalData
DeepLearning
Omics
9 days ago by
Physalia-courses
★ 2.6k
120,839 results • Page
2 of 2417
Recent Votes
Reproducibility Crisis
Comment: Shotgun dataset with polyG, low qualiity
Comment: Batch effect or biological difference
Comment: Inconsistency between VCF and HGVS
Answer: Lift over of GWAS summary stat file from Hg38 to Hg19
Answer: Lift over of GWAS summary stat file from Hg38 to Hg19
Answer: How do I install Terminal on Windows?
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shelkmike
★ 1.5k
Popular Question
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namck
• 0
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• 0
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Recent Replies
Comment: Associating VDJ clonotyping data with scRNA-seq in Seurat
by
garcesj
▴ 50
It's a great workaround. My only question is about just removing the duplicates (`tcr <- tcr[!duplicated(tcr$barcode), ]`). Aren't we losin…
Comment: Discrepancy between BAM and vcf
by
Istvan Albert
102k
I will also say that if you take any variant caller and then look at the corresponding BAM file, you'll find many minor inconsistencies - i…
Comment: Lift over of GWAS summary stat file from Hg38 to Hg19
by
Mllepnos
• 0
Thanks a lot for the recommendation to use bcftools +munge and +liftover instead of UCSC liftOver — I’ll definitely try that!
Comment: Discrepancy between BAM and vcf
by
GenoMax
150k
You could write to Illumina tech support and ask for resources that explain the default parameters for SNP calling/filtering in DRAGEN pipe…
Comment: Error gmx_mmpbsa: LP pseudo-atom is not supported
by
namck
• 0
Hi @bhavya2269, did you find any solution to this? I'm getting a similar error.
Comment: Question about `vg giraffe`
by
GenoMax
150k
You recent posts appear to be unrelated to the original question. If that is correct please post new questions in new threads. Posting unre…
Comment: Seeking Guidance on Selecting Control ChIP Sequences for nf-core/chipseq Pipelin
by
mark.ziemann
★ 2.0k
These are not really technical replicates if they simply re-sequenced the same library three times. Resequencing multiplexed libraries on d…
Comment: Question about `vg giraffe`
by
zhengluo
• 0
``` vg construct --reference ref.fa --vcf test.vcf.gz --alt-paths-plain --handle-sv --flat-alts --progress -t 100 > test.vg vg index --xg…
Answer: Difference in mapping rate when aligned with mapper.pl of miReep2 and bowtie1
by
wessel.willemsen
• 0
I had the same problem as you but i solved it by allowing the reads to map to more targets. By default mapper.pl does not allow a read to m…
Comment: Question about `vg giraffe`
by
zhengluo
• 0
Given a sample (sample1) with 100 insertions relative to the reference genome, can I identify which reads in the BAM file aligned to these …
Comment: Question about `vg giraffe`
by
zhengluo
• 0
I directly constructed the graph using VCF files and reference genome sequences through `vg construct`, but after converting it to GFA form…
Comment: How to introduce normalized and scaled seurat data into monocle 3?
by
Bastien Hervé
6.2k
For OP's question, my guess is that they got NA's because `ScaleData` is only called on the `VariableFeatures` found the step before. Try …
Answer: How to align library of highly similar sequences
by
ATpoint
87k
You need to deviate from the defaults of the aligner to enforce that only perfect matches are counted. Basically, and I use bowtie2 for pur…
Answer: Question about `vg giraffe`
by
Jouni Sirén
▴ 610
The easiest way is to align the reads to the graph in GAM or GAF format. Then you select sample `sample` as the reference using `vg gbwt`: …
Answer: How to introduce normalized and scaled seurat data into monocle 3?
by
Reza
• 0
I have a same question it seems that when we use the preprocess_cds() function, it does not save the normalized data directly in a separate…
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