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1,000 results • Page
3 of 20
Sort: Rank
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Votes
Replies
4
votes
6
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531
views
BLAST hits on viruses relate to different host than used
Phage
BLAST
Metagenomics
4 days ago by
DonPhager
• 0
0
votes
3
replies
332
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 4 days ago by
ATpoint
78k • written 5 days ago by
manuelmourato25
• 0
1
vote
4
replies
411
views
SNPs of a specific mouse strain
snp
updated 4 days ago by
Matthias Zepper
4.2k • written 5 days ago by
darklings
▴ 560
0
votes
0
replies
223
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
5 days ago by
Wenke
• 0
0
votes
3
replies
299
views
Annovar - Annotated file cells show string
annovar
5 days ago by
Roshan
• 0
2
votes
6
replies
458
views
Genotypes in vcf files
genotypes
vcf
updated 5 days ago by
Jeremy Leipzig
22k • written 5 days ago by
amy__
▴ 160
1
vote
1
reply
208
views
Genetic data QC prior to imputation
imputation
updated 5 days ago by
Raony Guimarães
★ 1.3k • written 5 days ago by
kl
▴ 10
4
votes
2
replies
267
views
Excel Pasting Question
Excel
updated 5 days ago by
Pierre Lindenbaum
158k • written 5 days ago by
Bweil2
▴ 10
0
votes
1
reply
236
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW
MinION
Nanopore
updated 4 days ago by
GenoMax
136k • written 5 days ago by
Soumajit
▴ 40
0
votes
0
replies
155
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
5 days ago by
bioinfo
▴ 60
6
votes
5
replies
3.0k
views
Multi threading bowtie index
bowtie
indexing
updated 5 days ago by
colindaven
5.7k • written 8.2 years ago by
ChillarAnand
▴ 70
2
votes
4
replies
350
views
Human mitochondrial reference genome
reference
genome
mitochondria
1 day ago by
singhankit973
• 0
0
votes
0
replies
155
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA
Worms
RNA-Seq
5 days ago by
kdca
• 0
0
votes
3
replies
267
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
5 days ago by
Sara
▴ 230
0
votes
0
replies
874
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics
telomeres
reads
5 days ago by
Mark
• 0
1
vote
3
replies
1.1k
views
DoubletFinder for Python?
scanpy
doublets
scrublet
updated 5 days ago by
fracarb8
★ 1.3k • written 10 months ago by
aerlaut
▴ 10
0
votes
0
replies
151
views
not best k value found
de
assemblly
assembly
novo
kmergenie
5 days ago by
shaileshdesai76
• 0
7
votes
5
replies
1.4k
views
How to learn Scanpy
scanpy
Python
rna-seq
updated 5 days ago by
Prakki Rama
★ 2.7k • written 17 months ago by
godwin
▴ 30
4
votes
4
replies
469
views
Is there a good software to generate test genomics data?
genomics
testing
benchmarking
updated 5 days ago by
Brian Bushnell
19k • written 7 days ago by
Mark
• 0
3
votes
4
replies
362
views
selection of reference genome
hg19
reference
genome
hg38
4 days ago by
Tsin-Lau
• 0
1
vote
4
replies
593
views
Forum:
Current Trends in Bioinformatics
structural-bioinformatics
updated 5 days ago by
ATpoint
78k • written 22 days ago by
Paulo
• 0
1
vote
1
reply
292
views
After merging batches, I got very segmented umap in scanpy
scanpy
single-cell
5 days ago by
MohammadAlkadi
▴ 70
0
votes
0
replies
159
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR
ribo-seq
multi-mapped
rna-seq
TE
6 days ago by
Carmen
• 0
0
votes
0
replies
166
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq
deseq2
6 days ago by
pl23
• 0
2
votes
12
replies
842
views
BCL2FASTQ: Segmentation Fault Error (segfault)
linux
Segmentation-fault
bcl2fastq
6 days ago by
gillhuberfelix
▴ 20
5
votes
5
replies
6.1k
views
6 follow
Mitochondrial genes in single cell nuclear RNAseq data
RNA-Seq
gene
mitochondria
updated 6 days ago by
Prakki Rama
★ 2.7k • written 4.9 years ago by
dalhoomist
▴ 40
0
votes
2
replies
272
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
1 day ago by
je71xusa
• 0
0
votes
2
replies
265
views
Tool to get genes in the neighbourhood of a particular gene
locus
Gene
updated 6 days ago by
Raony Guimarães
★ 1.3k • written 6 days ago by
ThePlaintiff
▴ 80
0
votes
0
replies
170
views
News:
GWAS course
R
Bioinformatics
GWAS
6 days ago by
carlopecoraro2
★ 2.4k
2
votes
3
replies
373
views
Salmon index problem
Salmon
docker
RNAseq
index
refgenie
updated 5 days ago by
Raony Guimarães
★ 1.3k • written 6 days ago by
enee
▴ 10
9
votes
4
replies
2.1k
views
Tool:
SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files containing DNA and protein sequences
fasta
sequences
java
6 days ago by
Hugo
▴ 380
2
votes
3
replies
332
views
BWA mem align reads with MQ = 0 to only one region (reference genome has two similar sequences).
NGS
BWA
updated 6 days ago by
Raony Guimarães
★ 1.3k • written 6 days ago by
captainlabman
▴ 10
2
votes
2
replies
306
views
Merging several vcf files for GWAS?
R
beginner
gwas
ngs
novogene
6 days ago by
sabrilo171
▴ 10
7
votes
5
replies
313
views
bcftools error: : error while loading shared libraries: libcrypto.so.1.0.0:
bcftools
5 days ago by
jiyoung
▴ 20
2
votes
9
replies
596
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
45 minutes ago by
ian.will
▴ 10
2
votes
2
replies
472
views
Help with scvelo
scvelo
updated 6 days ago by
Prakki Rama
★ 2.7k • written 6 weeks ago by
Chris
▴ 230
5
votes
2
replies
239
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
5 days ago by
Rafael Soler
★ 1.2k
1
vote
9
replies
2.7k
views
PCAtools data file not linking to metadata file
R
PCA
RNA-Seq
PCAtools
updated 6 days ago by
ATpoint
78k • written 3.4 years ago by
bryce.plu
▴ 10
1
vote
0
replies
207
views
Job:
Fully funded PhD positions, Vienna, Austria
fully-funded
phd
updated 6 days ago by
colindaven
5.7k • written 6 days ago by
facultyrecruiting.ista
▴ 10
0
votes
2
replies
260
views
Use of IDR after running MACS3 for ATAC-seq data
ATAC-seq
MACS2
MACS3
3 days ago by
Orange
▴ 10
2
votes
2
replies
209
views
how do I assemble centromere regions in a plant genome?
novo
de
assembly
updated 6 days ago by
WouterDeCoster
47k • written 6 days ago by
evyk
• 0
4
votes
9
replies
566
views
Working with NCBI downloadable Datasets
NCBI
Genedata
Datasets
updated 1 day ago by
rfran010
▴ 880 • written 7 days ago by
jakob.olsson04
• 0
1
vote
2
replies
192
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole
genome
assembly
sequencing
updated 6 days ago by
WouterDeCoster
47k • written 6 days ago by
manaswiniparija3
▴ 10
1
vote
0
replies
136
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
6 days ago by
WUSCHEL
▴ 720
8
votes
6
replies
478
views
How to filter .fasta file based on conditional statement
abundance
filtering
fasta
vsearch
updated 6 days ago by
Brian Bushnell
19k • written 7 days ago by
rob_DNA
▴ 20
0
votes
3
replies
283
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 1 day ago by
jv
★ 1.2k • written 7 days ago by
TC_Chang
▴ 10
0
votes
0
replies
108
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway
mapping
database
7 days ago by
Ngrin
• 0
0
votes
0
replies
120
views
GenAlEx Haploid Data Detecting Recombination
GenAlEx
Popgen
Haploid
Recombination
7 days ago by
turcoa1
• 0
2
votes
1
reply
172
views
What is Bowtie2 --norc parameter?
bowtie2
norc
alignment
updated 7 days ago by
ATpoint
78k • written 7 days ago by
lvl2111
• 0
3
votes
2
replies
231
views
Find all locations of aligned reads with MQ (Mapping Quality) = 0.
align
IGV
BAM
updated 7 days ago by
Brian Bushnell
19k • written 7 days ago by
captainlabman
▴ 10
1,000 results • Page
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Recent Votes
Comment: Merging several vcf files for GWAS?
Comment: p-value combination methods
Comment: bwa mem hangs after a few thousand reads
Comment: bwa mem hangs after a few thousand reads
How to make a survival plot for a gene between High expression and low expression samples?
Comment: bwa mem hangs after a few thousand reads
bwa mem hangs after a few thousand reads
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Recent Replies
Comment: Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
by
ian.will
▴ 10
Yep gave that a go and proceeding with the analysis. Thanks again.
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
DINESHR
• 0
Regarding Diffbind, How does diffbind calculate common peaks with the samples. I'm observing that certain peaks identified as common using …
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
rpolicastro
12k
Assuming Cell Ranger was ran correctly it's unlikely that the sample is useable. It looks like most droplets were probably empty.
Comment: bwa mem hangs after a few thousand reads
by
cee28
▴ 30
Here is the output with the "-v 4" flag (not showing all the @SQ comments) : > @SQ SN:chrUn_GL000214v1 LN:137718 @SQ SN:chrUn_KI270742v1 L…
Answer: Where is the index command?
by
Michael
53k
There is a ready-made package for samtools, simply do apt install samtools Also, your screenshot shows you are using the root account…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 180
Use option `-v` with value of 4 or above to help diagnose the issue: `-v INT` Control the verbose level of the output. This option has not…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 180
Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Thank you, I really appreciate your insight! I will look into the dropouts I have.
Comment: Generate Read counts from bam file
by
NextGenSeek
• 0
Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper?
by
GenoMax
136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods
by
i.sudbery
18k
edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
Answer: What type of cancer did they study in this paper?
by
jared.andrews07
★ 16k
Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
Comment: p-value combination methods
by
sehriban.buyukkilic
• 0
its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba
by
el24
▴ 40
Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
Comment: Match variants for allele frequency, LD score, and other features
by
Jautis
▴ 520
Trying to bump this
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