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941 results • Page
2 of 19
Sort: Rank
Rank
Views
Votes
Replies
1
vote
4
replies
232
views
Artificial reads - remove multiple mapped reads against reference genome, and only keep reads that completely match without any mismatches - samtools
samtools
2 days ago by
Agamemnon
▴ 60
0
votes
0
replies
81
views
Haploview linkage format .ped and .info file error
plink
Haploview
vcftool
3 days ago by
Nai
▴ 50
0
votes
0
replies
116
views
Bcftools consensus generates mismatched consensus sequence
Consensus
sequence
3 days ago by
Duy
• 0
0
votes
0
replies
82
views
Is there a function to get the number of aligned sites between pairs of sequences in a multiple sequence alignment in R?
msa
R
3 days ago by
audrey
• 0
0
votes
0
replies
101
views
Nucleotide substitution model and neighbor-joining tree
phylogeny
substitution
mega
neighbor-joining
modeltest
2 days ago by
poecile.pal
▴ 50
0
votes
0
replies
101
views
Octopus advanced vcf guide: Example of overlapping vcf calls with *
vcf
spanning
alleles
octopus
3 days ago by
penington.j
• 0
0
votes
0
replies
132
views
Link products to their genes
RNA-SEQ
GO
edgeR
3 days ago by
Pegasus
▴ 80
0
votes
0
replies
129
views
Trajectory analysis using Monocle3 with Seurat sub-clustering
scRNA-seq
Trajectory
Seurat
analysis
Monocle3
3 days ago by
joonhong kwon
▴ 40
0
votes
1
reply
183
views
Error parsing strand (?) from GFF line
assembly
updated 3 days ago by
cmdcolin
★ 2.9k • written 4 days ago by
hafiz.talhamalik
▴ 350
1
vote
0
replies
141
views
List of Ongoing and Planned Long Read Sequencing studies?
long-read-sequencing
third-generation
updated 4 days ago by
Ram
38k • written 4 days ago by
Vincent Laufer
★ 2.6k
0
votes
1
reply
166
views
SNP ID (rsID) to Chr no. and Position
Annotation
4 days ago by
Jewahir
• 0
0
votes
0
replies
127
views
how to plot distribution of SNPs across a set of genes based on distance between snp and gene
snp
genes
updated 4 days ago by
Ram
38k • written 4 days ago by
rheab1230
▴ 140
0
votes
0
replies
113
views
Reactome Species Comparison - analysis table
reactome
3 days ago by
a11msp
▴ 120
0
votes
1
reply
157
views
Using multimaping reads or unique reads on featurecounts?
featurecounts
HISAT2
updated 4 days ago by
GenoMax
127k • written 4 days ago by
omargmc.tak
• 0
0
votes
0
replies
100
views
How to import impute2.dosage files to analyse it in R (GWAS)
regression
GWAS
impute2
dosage
4 days ago by
Sebastian
• 0
0
votes
0
replies
102
views
Michigan Imputation server failed job
michigan-imputation-server
vcf
updated 4 days ago by
Ram
38k • written 4 days ago by
Najla
• 0
0
votes
0
replies
99
views
MD simulation error
MD
schrodinger
updated 4 days ago by
Ram
38k • written 4 days ago by
mixmatchey
• 0
0
votes
0
replies
106
views
File has zero value indivuals
Haploview
updated 4 days ago by
Ram
38k • written 4 days ago by
Nai
▴ 50
0
votes
6
replies
408
views
Kallisto bustools for scRNA-seq
Kallisto
updated 2 days ago by
dsull
★ 4.0k • written 4 days ago by
t.ru
▴ 20
0
votes
0
replies
137
views
KEGGList Error in R
KEGGList
4 days ago by
GiV17
▴ 50
0
votes
0
replies
123
views
GATK VariantAnnotator -A PossibleDeNovo
VariantAnnotator
GATK
4 days ago by
zihanss
• 0
0
votes
4
replies
735
views
MapSplice2 gives error if the thread count (-p value) is greater than 2
Mapsplice2
fusion_candidates
updated 4 days ago by
GenoMax
127k • written 20 months ago by
nkmalini97
• 0
0
votes
0
replies
120
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
5 days ago by
poecile.pal
▴ 50
0
votes
0
replies
187
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
5 days ago by
sharmatina189059
▴ 110
1
vote
4
replies
264
views
Protein name in GenBank
genbank
python
biopython
updated 5 days ago by
GenoMax
127k • written 5 days ago by
Daniel
• 0
0
votes
1
reply
191
views
doing PBS(population branch statistics) in ANGSD
fst
pbs
ANGSD
3 days ago by
Blessing
• 0
0
votes
1
reply
176
views
Tell me about making a transcriptome model of a specific tissue.
model
transcriptome
updated 5 days ago by
ATpoint
71k • written 5 days ago by
Soliloquy
▴ 10
0
votes
0
replies
171
views
How to fix FreeBayes error "unable to find FASTA index entry for bed files"
calling
freebayes
variant
RNA-Seq
5 days ago by
wlei091226
• 0
0
votes
1
reply
197
views
how to import hdf5 Hi-C data into R using HiTC package
hdf5
importC
R
HiTC
updated 6 days ago by
rpolicastro
11k • written 6 days ago by
rheab1230
▴ 140
0
votes
0
replies
158
views
Emapplot Pie Graphic Legend Interferes with Map
enrichplot
clusterprofiler
Emapplot
6 days ago by
raquel.ajalik
• 0
1
vote
0
replies
165
views
Minimap2 giving opposite strand orientation than Pychopper
nanopore
Pychopper
Minimap2
6 days ago by
vanda.gaonach-lovejoy
▴ 10
0
votes
4
replies
347
views
RNA Sequencing and Vg pan -transcriptome build
fasta
pan-transcriptome
pan-genome
vg
3 days ago by
kcarery
• 0
0
votes
0
replies
164
views
What is the meaning of 'a too large, ITMAX too small in gamma countinued fraction (gcf)'
meta
analysis
GWAS
METAL
updated 6 days ago by
GenoMax
127k • written 6 days ago by
ymberzal
• 0
0
votes
4
replies
414
views
Problem with fatsq-dump
fastq-dump
sratoolkit
5 days ago by
Utpal
• 0
0
votes
0
replies
171
views
ERROR using CIBERSORTx Docker version
deconvolution
version
Docker
CIBERSORTx
4 days ago by
Leite
★ 1.2k
0
votes
2
replies
255
views
Ortholog assembly and extraction
geneious
Ortholog
blast
updated 7 days ago by
dthorbur
▴ 420 • written 7 days ago by
bagdiev39
• 0
0
votes
2
replies
224
views
lncTar
LncRNA
lncTar
maize
updated 7 days ago by
Ram
38k • written 7 days ago by
Amrendra
• 0
1
vote
3
replies
1.0k
views
LncTar error
LncRNA
LncTar
mRNA
updated 7 days ago by
Ram
38k • written 2.1 years ago by
kuntalasb
▴ 10
0
votes
2
replies
254
views
chloroplast genome gaps
genome
gaps
chloroplast
7 days ago by
ugur
• 0
0
votes
0
replies
143
views
Using Lastz aligner
aligner
genome
Lastz
updated 7 days ago by
GenoMax
127k • written 7 days ago by
Diego
▴ 90
1
vote
0
replies
137
views
How to calculate Exon-Intron junction perbase coverage?
RNA-Seq
bedtools
7 days ago by
barrypraveen
▴ 110
0
votes
0
replies
155
views
Extract/include transcript list from GAGE analysis result
RNAseq
GAGE
4 days ago by
farzaneafzali
▴ 70
0
votes
0
replies
131
views
Bam-readcount-installation error
bam-readcount
updated 7 days ago by
Pierre Lindenbaum
153k • written 7 days ago by
shreshta2396
• 0
0
votes
0
replies
124
views
issue changing k values on SOAPdenovo2
novo
de
assembly
7 days ago by
parrasevilla.bioinfo
• 0
0
votes
1
reply
226
views
normalized score for SpatialFeaturePlot
Spatial
Transcriptome
normalization
integration
Seurat
updated 7 days ago by
jv
★ 1.0k • written 7 days ago by
Omics data mining
▴ 210
1
vote
3
replies
353
views
SKAT in R
pvalue
skat
snp
5 days ago by
Eliza
▴ 20
1
vote
2
replies
275
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 7 days ago by
i.sudbery
16k • written 8 days ago by
rls_08
▴ 40
0
votes
2
replies
219
views
No Passing Variants GATK
calling
variantcalling
GATK
variant
8 days ago by
brandnewatthis
• 0
0
votes
0
replies
225
views
How to calculate the correlation between the expression levels of two genes (features) with Seurat package in scRNA-seq data?
scRNA-seq
Seurat
7 days ago by
sunyeping
▴ 80
0
votes
1
reply
184
views
Gaia CNV error TCGA data
CNV
GAIA
TCGA
updated 8 days ago by
Ram
38k • written 8 days ago by
s.lueong
• 0
941 results • Page
2 of 19
Recent Votes
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
Answer: Getting Intron Positions from Amino Acid Sequences
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Comment: How to deal with the probe id mapping to multiple gene ids?
by
GenoMax
127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
by
rpolicastro
11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created
by
DdogBoss
• 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate
by
ATpoint
71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate
by
Ram
38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis
by
rpolicastro
11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files
by
Darrenjdd
• 0
Perfect! Thank you!
Comment: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
by
Daniel
• 0
Hi, I am wondering if you ever got an answer for this question. Also, I am curious why it is true that "All the reads coming from one end…
Answer: how can i filter a sam file from a paf file
by
Trivas
▴ 750
A quick search shows that `paf2sam` doesn't exist because a `.paf` file doesn't contain the CIGAR strings that `.sam` files have. A work ar…
Comment: What is the major problem with this pipeline of SNPs analysis?
by
Ram
38k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: What is the major problem with this pipeline of SNPs analysis?
by
Pierre Lindenbaum
153k
you can stick to gatk. But, again, using a GVCF without GenotypeGVCF is meaningless
Comment: Getting Intron Positions from Amino Acid Sequences
by
fafad046
• 0
thank you so so much, it worked! you are an absolute life savior :D
Answer: Getting Intron Positions from Amino Acid Sequences
by
GenoMax
127k
Using [**EntrezDirect**][1] (truncated because of space): $ esearch -db protein -query NP_001243728.1 | elink -target gene | efetch …
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