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83 results • Page
1 of 2
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Views
Votes
Replies
0
votes
0
replies
14
views
constructing pangenome through psvcp
psvcp
pangenome
52 minutes ago by
analyst
▴ 50
0
votes
2
replies
25
views
zero TPM for many gene including housekeeping when using kallisto
RNAseq
updated 10 minutes ago by
ATpoint
82k • written 1 hour ago by
ashkan
▴ 160
0
votes
1
reply
19
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated just now by
dthorbur
★ 2.0k • written 1 hour ago by
Umer
▴ 50
0
votes
2
replies
111
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 2 hours ago by
Pierre Lindenbaum
161k • written 9 hours ago by
melissachua90
▴ 70
0
votes
0
replies
40
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
4 hours ago by
Varsha
• 0
0
votes
1
reply
100
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 21 minutes ago by
GenoMax
142k • written 8 hours ago by
huxiangyulove
• 0
0
votes
0
replies
61
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
11 hours ago by
O.rka
▴ 720
0
votes
0
replies
63
views
Help! Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
11 hours ago by
BATMAN
• 0
0
votes
4
replies
210
views
Merge clusters in Seurat UMAP
seurat
umap
2 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
65
views
Use of ichor CNA
Dog
CNA
genome
16 hours ago by
sainavyav22
• 0
2
votes
2
replies
171
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 14 hours ago by
Ram
43k • written 17 hours ago by
txema.heredia
▴ 130
0
votes
0
replies
72
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
19 hours ago by
Jsarria.EEAD
• 0
0
votes
1
reply
120
views
How can I calculate the OS of each patient?
overall-survival
updated 19 hours ago by
ATpoint
82k • written 19 hours ago by
Pedro
• 0
0
votes
0
replies
72
views
cat-bgen fail
bgenix
updated 19 hours ago by
Ram
43k • written 20 hours ago by
lambard
• 0
1
vote
1
reply
126
views
API kegg - IndexError: list index out of range
kegg
API
updated 7 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
mirwa.zidi93
• 0
0
votes
0
replies
82
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
1 day ago by
ebertomeup
• 0
0
votes
3
replies
198
views
Sam file Header problem
Sam
Header
problem
file
updated 3 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
saifulislam99121
• 0
0
votes
0
replies
93
views
select set of intervals that cover a genomic region
GRanges
bed
1 day ago by
ntsopoul
▴ 60
0
votes
1
reply
118
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 5 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Luqman
• 0
0
votes
2
replies
154
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
0
votes
1
reply
148
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 1 day ago by
Michael
54k • written 1 day ago by
mgranada3
▴ 30
0
votes
1
reply
134
views
Add line under stat test
stats
R
updated 7 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Ghada
• 0
0
votes
0
replies
99
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Rodolfo Adrián
• 0
1
vote
14
replies
596
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
4 hours ago by
hophuquy0944
• 0
0
votes
1
reply
136
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
1 day ago by
asalimih
▴ 60
0
votes
0
replies
107
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
1 day ago by
jway
• 0
0
votes
1
reply
144
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 23 hours ago by
Papyrus
★ 2.9k • written 1 day ago by
yura.grabovska
▴ 90
0
votes
1
reply
146
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 20 hours ago by
GenoMax
142k • written 1 day ago by
Lélé
▴ 10
0
votes
3
replies
161
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
1 day ago by
Esraa
• 0
0
votes
0
replies
92
views
ReactomeGSA
ReactomeGSA
2 days ago by
Shaimaa Gamal
▴ 10
0
votes
5
replies
278
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 1 day ago by
GenoMax
142k • written 2 days ago by
chrisk
• 0
0
votes
2
replies
163
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 23 hours ago by
DGTool
▴ 20 • written 2 days ago by
iqra
• 0
0
votes
0
replies
98
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Dude
• 0
0
votes
0
replies
95
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
2 days ago by
brunofelicianodeomena
• 0
0
votes
1
reply
143
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
2 days ago by
sansan_96
▴ 90
1
vote
2
replies
222
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
18 hours ago by
bioinfo
▴ 150
0
votes
2
replies
186
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
2 days ago by
melissa.joubert
• 0
0
votes
0
replies
109
views
Is there a real ground truth for CNV data?
CNV
2 days ago by
jennyp0706
• 0
1
vote
1
reply
145
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
kilcdincer
▴ 10
0
votes
3
replies
200
views
How to access GWAVA software of data
GWAVA
updated 2 days ago by
GenoMax
142k • written 3 days ago by
nonaddldy
▴ 10
0
votes
0
replies
93
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
3 days ago by
Spring
• 0
0
votes
2
replies
175
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
3 days ago by
IdaHao0921
• 0
0
votes
3
replies
342
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
160
views
How to process Bulk WES data?
WES
WGS
updated 3 days ago by
GenoMax
142k • written 3 days ago by
wyuan37
• 0
0
votes
1
reply
160
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 3 days ago by
GenoMax
142k • written 3 days ago by
cedric.blais
• 0
0
votes
1
reply
149
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 3 days ago by
Ram
43k • written 3 days ago by
eking28
• 0
0
votes
0
replies
104
views
reference-free assembly error assessment tools
assembly
3 days ago by
lagartija
▴ 160
0
votes
4
replies
257
views
Galaxy StringTie error
stringtie
galaxy
3 days ago by
trkfs
• 0
0
votes
0
replies
103
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
3 days ago by
atariw
▴ 10
1
vote
4
replies
341
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 2 days ago by
Juke34
8.6k • written 3 days ago by
Vijith
▴ 30
83 results • Page
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Answer: Generating consensus sequence from bam file
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Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
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Recent Replies
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
dariober
14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err
by
GenoMax
142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input?
by
Pierre Lindenbaum
161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem
by
Pierre Lindenbaum
161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
DGTool
▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
b.contreras.moreira
▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input?
by
LucisTheFather
• 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
thank you
Comment: How to extract cells of different species after mapping with combined genome?
by
Tony
• 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
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