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1,000 results • Page
2 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
118
views
TrN (df = k+5) and TrNe (df = k+2) - which of these Tamura-Nei model variants is used in MEGAx?
Tamura-Nei
phylogeny
phangorn
modelTest
mega
3 days ago by
poecile.pal
▴ 50
0
votes
0
replies
185
views
How to sort graph based on fold change and instead of activated and suppressed, how to add up and downregulated in graph header?
clusterprofiler
3 days ago by
sharmatina189059
▴ 110
1
vote
4
replies
258
views
Protein name in GenBank
genbank
python
biopython
updated 3 days ago by
GenoMax
127k • written 3 days ago by
Daniel
• 0
0
votes
1
reply
184
views
doing PBS(population branch statistics) in ANGSD
fst
pbs
ANGSD
1 day ago by
Blessing
• 0
0
votes
1
reply
171
views
Tell me about making a transcriptome model of a specific tissue.
model
transcriptome
updated 3 days ago by
ATpoint
70k • written 3 days ago by
Soliloquy
▴ 10
0
votes
0
replies
167
views
How to fix FreeBayes error "unable to find FASTA index entry for bed files"
calling
freebayes
variant
RNA-Seq
3 days ago by
wlei091226
• 0
0
votes
1
reply
193
views
how to import hdf5 Hi-C data into R using HiTC package
hdf5
importC
R
HiTC
updated 4 days ago by
rpolicastro
11k • written 4 days ago by
rheab1230
▴ 140
0
votes
0
replies
157
views
Emapplot Pie Graphic Legend Interferes with Map
enrichplot
clusterprofiler
Emapplot
4 days ago by
raquel.ajalik
• 0
1
vote
0
replies
164
views
Minimap2 giving opposite strand orientation than Pychopper
nanopore
Pychopper
Minimap2
4 days ago by
vanda.gaonach-lovejoy
▴ 10
0
votes
4
replies
337
views
RNA Sequencing and Vg pan -transcriptome build
fasta
pan-transcriptome
pan-genome
vg
1 day ago by
kcarery
• 0
0
votes
0
replies
163
views
What is the meaning of 'a too large, ITMAX too small in gamma countinued fraction (gcf)'
meta
analysis
GWAS
METAL
updated 4 days ago by
GenoMax
127k • written 4 days ago by
ymberzal
• 0
0
votes
4
replies
398
views
Problem with fatsq-dump
fastq-dump
sratoolkit
3 days ago by
Utpal
• 0
0
votes
0
replies
160
views
ERROR using CIBERSORTx Docker version
deconvolution
version
Docker
CIBERSORTx
2 days ago by
Leite
★ 1.2k
0
votes
2
replies
250
views
Ortholog assembly and extraction
geneious
Ortholog
blast
updated 5 days ago by
dthorbur
▴ 420 • written 5 days ago by
bagdiev39
• 0
0
votes
2
replies
222
views
lncTar
LncRNA
lncTar
maize
updated 5 days ago by
Ram
38k • written 5 days ago by
Amrendra
• 0
1
vote
3
replies
1.0k
views
LncTar error
LncRNA
LncTar
mRNA
updated 5 days ago by
Ram
38k • written 2.1 years ago by
kuntalasb
▴ 10
0
votes
2
replies
252
views
chloroplast genome gaps
genome
gaps
chloroplast
5 days ago by
ugur
• 0
0
votes
0
replies
141
views
Using Lastz aligner
aligner
genome
Lastz
updated 5 days ago by
GenoMax
127k • written 5 days ago by
Diego
▴ 90
1
vote
0
replies
133
views
How to calculate Exon-Intron junction perbase coverage?
RNA-Seq
bedtools
5 days ago by
barrypraveen
▴ 110
0
votes
0
replies
148
views
Extract/include transcript list from GAGE analysis result
RNAseq
GAGE
2 days ago by
farzaneafzali
▴ 70
0
votes
0
replies
129
views
Bam-readcount-installation error
bam-readcount
updated 5 days ago by
Pierre Lindenbaum
153k • written 5 days ago by
shreshta2396
• 0
0
votes
0
replies
122
views
issue changing k values on SOAPdenovo2
novo
de
assembly
5 days ago by
parrasevilla.bioinfo
• 0
0
votes
1
reply
218
views
normalized score for SpatialFeaturePlot
Spatial
Transcriptome
normalization
integration
Seurat
updated 5 days ago by
jv
★ 1.0k • written 5 days ago by
Omics data mining
▴ 210
1
vote
3
replies
343
views
SKAT in R
pvalue
skat
snp
3 days ago by
Eliza
▴ 20
1
vote
2
replies
271
views
in an RNA-seq experiment, what threshold would you use to define a set of expressed or active genes in a cell line?
RNA-seq
updated 5 days ago by
i.sudbery
16k • written 6 days ago by
rls_08
▴ 40
0
votes
2
replies
215
views
No Passing Variants GATK
calling
variantcalling
GATK
variant
6 days ago by
brandnewatthis
• 0
0
votes
0
replies
217
views
How to calculate the correlation between the expression levels of two genes (features) with Seurat package in scRNA-seq data?
scRNA-seq
Seurat
5 days ago by
sunyeping
▴ 80
0
votes
1
reply
181
views
Gaia CNV error TCGA data
CNV
GAIA
TCGA
updated 6 days ago by
Ram
38k • written 6 days ago by
s.lueong
• 0
0
votes
0
replies
132
views
BULK mRNA-seq with UMIs. Does it make sense to run bedtools genomecov?
RNAseq
gene-length
normalization
6 days ago by
txema.heredia
▴ 70
0
votes
0
replies
121
views
Deeptools clustering differs when clustering sample as standalone and together with other samples
deepTools
6 days ago by
jordi.planells
▴ 450
2
votes
6
replies
317
views
bioinformatics problems solved by graphs data structure
Graph
algorithm
data-structure
updated 6 days ago by
Ram
38k • written 6 days ago by
abdelmalek.benmeziane
• 0
0
votes
1
reply
140
views
Embedded stop codon in translated nucleotide sequences in DAMBE
DAMBE
stop-codon
updated 6 days ago by
Mensur Dlakic
★ 23k • written 6 days ago by
Fathima
• 0
0
votes
1
reply
156
views
ImportError: Bio.Alphabet has been removed from Biopython
Biopython
updated 6 days ago by
Wayne
★ 1.7k • written 6 days ago by
Neel
▴ 10
0
votes
0
replies
112
views
Can't initialise orthomcl schema at orthomclInstallschema step.
mysql
perl
orthomcl
6 days ago by
shivankparashar
• 0
3
votes
2
replies
224
views
correlations in R
cor
R
6 days ago by
rene.j.erhardt
▴ 20
1
vote
2
replies
226
views
Weird looking dispersion & MA plot?
deseq2
RNA-seq
updated 6 days ago by
Ram
38k • written 7 days ago by
Neha
• 0
2
votes
4
replies
252
views
Error with a function in ATAC-seq analysis
ATAC-seq
6 days ago by
Chris
▴ 70
0
votes
0
replies
119
views
how to get genomic range for hi-c datasets in hdf5 file
R
hi-c
contact-map
genomic-ranges
updated 6 days ago by
Ram
38k • written 7 days ago by
rheab1230
▴ 140
0
votes
0
replies
130
views
Samtools: remove unmapped reads as well as reads that are mapped incorrectly
samtools
updated 7 days ago by
Ram
38k • written 7 days ago by
npavliukovec
• 0
0
votes
0
replies
104
views
how to interpret hi-c heatmap hdf5 file
heatmap
maps
hdf5
hi-c
7 days ago by
rheab1230
▴ 140
2
votes
12
replies
551
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 5 days ago by
Ram
38k • written 7 days ago by
Human
• 0
0
votes
0
replies
105
views
Gain of function amplifications - CCLE/cBioPortal
copy
gains
amplification
number
cBioPortal
CCLE
7 days ago by
Lakshmi
▴ 10
0
votes
0
replies
102
views
Biomark Fluidigm delta delta CT method calculation
Fluidigm
Biomark
qPCR
7 days ago by
jms2520
▴ 20
0
votes
0
replies
94
views
pyscenic cannot mapped to the feather file
pyscenic
7 days ago by
Andy
▴ 30
0
votes
0
replies
88
views
How to calculate Summary.csv statistics after re-running STARSolo cell filtering?
scRNA-seq
STARSolo
STAR
7 days ago by
ayeTown
• 0
0
votes
0
replies
97
views
Solving set of equations possibly with Matlab for affinity measurement with ELISA
set
ELISA
affinity
Matlab
equation
7 days ago by
field654
▴ 30
0
votes
0
replies
100
views
how to get the nucleotide squence behind a symbolic ALT in VCF
SV
vcf
sniffles
5 days ago by
Maxine
• 0
0
votes
0
replies
155
views
How can I retrive the actual amino acid and the alternative amino acid (if any cordon changes happened due to editing)?
RNA
editing
7 days ago by
Genetics
▴ 20
0
votes
0
replies
92
views
pyscenic feather file
pyscenic
7 days ago by
Andy
▴ 30
1
vote
1
reply
154
views
Is there a site that takes a list of uniprot IDs/gene IDs as input and create radial phylogenetic tree?
phylogenetictree
7 days ago by
Diwan
▴ 650
1,000 results • Page
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Recent Votes
Answer: Variant caller reports a homozygous variant genotype, but more reads are associa
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
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Comment: GO enrichment analysis
Comment: GO enrichment analysis
Answer: What is the NCBI's definition of an "atypical genome"?
A: Why is RNA-Seq or cDNA used to detect gene fusions instead of gDNA?
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Recent Replies
Answer: Any tips in landing a bioinformatic job?
by
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★ 2.5k
Do you have a public facing github page (or equivalent) that provides examples of bioinformatics workflows you've created? For myself, if …
Comment: Align miRNA library (small RNA-seq) without trimming
by
Paola
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Hi Ming Untrimmed reads have 76bp in average.
Answer: Align miRNA library (small RNA-seq) without trimming
by
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bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Comment: Differences in RNAseq Variant Calling and Allele Specific Expression
by
afei
• 0
Hi! I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
Comment: Variant caller reports a homozygous variant genotype, but more reads are associa
by
rebeliscu
▴ 50
Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made. Thanks for you…
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
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cfos4698
▴ 730
To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example: ``` bcftools …
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Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
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• 0
I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Answer: Total No of Genes of GENCODE Release 43
by
ahmad
• 0
The following is the correct code gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43
by
ahmad
• 0
Hello, thanks for replying, by mistake I paste the wrong code. the following is the corrected gtf_43<-rtracklayer::import('gencode.v43…
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I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
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First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
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There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
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Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
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