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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
135
views
KEGGList Error in R
KEGGList
2 days ago by
GiV17
▴ 50
0
votes
1
reply
218
views
How to analyze RepeatProteinMask results
RepeatProteinMask
2 days ago by
zijian
• 0
0
votes
1
reply
287
views
how to look at interaction between SNP and gene
SNP
Gene
Hi-C
updated 2 days ago by
Ram
38k • written 6 days ago by
rheab1230
▴ 140
1
vote
2
replies
343
views
Remove part of headers in FASTA file
Fasta
updated 2 days ago by
Mark
★ 1.2k • written 4 days ago by
fatemeh
• 0
0
votes
2
replies
214
views
How to get a list of genes information for a pathway?
pathway
updated 2 days ago by
ATpoint
70k • written 2 days ago by
WUSCHEL
▴ 720
0
votes
0
replies
122
views
GATK VariantAnnotator -A PossibleDeNovo
VariantAnnotator
GATK
2 days ago by
zihanss
• 0
0
votes
0
replies
120
views
Tool:
BioLabImage - Mac program for DNA/RNA/protein gel/blot, cells/colonies image analysis
image-analysis
gel
blot
cells
colonies
updated 2 days ago by
Ram
38k • written 2 days ago by
vytarasov
▴ 180
0
votes
1
reply
291
views
getTable ignores query ranges
rtracklayer
2 days ago by
Kyle
▴ 10
0
votes
2
replies
255
views
Installing rlang version 1.1.0
ExomeDepth
rlang
R
2 days ago by
Medha
• 0
3
votes
2
replies
183
views
Somatic truth set
benchmarking
Somatic
updated 5 hours ago by
lethalfang
▴ 90 • written 3 days ago by
samuel
▴ 210
5
votes
5
replies
447
views
GetBM - GERP conservation score for GRCm39
ensembl
biomaRt
updated 2 days ago by
GenoMax
127k • written 5 days ago by
Kyle
▴ 10
0
votes
0
replies
178
views
Job:
Bioinformatician - Cancer Research (Melbourne, Australia)
single-cell
RNAseq
3 days ago by
ahnje770
▴ 20
0
votes
4
replies
733
views
MapSplice2 gives error if the thread count (-p value) is greater than 2
Mapsplice2
fusion_candidates
updated 2 days ago by
GenoMax
127k • written 20 months ago by
nkmalini97
• 0
2
votes
1
reply
190
views
Confused on strandedness, what are antisense transcripts?
rnaseq
strandedness
updated 2 days ago by
dsull
★ 4.0k • written 3 days ago by
coboyfan12
• 0
4
votes
4
replies
245
views
Hard clip fastq
fastq
updated 3 days ago by
GenoMax
127k • written 3 days ago by
samuel
▴ 210
0
votes
1
reply
183
views
using GRanges metadata to constrain overlap searches between objects
plyranges
Bioconductor
GRanges
R
GenomicRanges
updated 2 days ago by
seidel
11k • written 3 days ago by
Charles Murtaugh
▴ 40
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
1
reply
264
views
Adding median value to VlnPlot in Seurat
Median
Seurat
updated 3 days ago by
seidel
11k • written 4 days ago by
Swati
• 0
0
votes
3
replies
327
views
how to know what adapter sequences to trim for RNA-seq?
fastq
RNA-seq
cutadapt
3 days ago by
lunarskye222
• 0
0
votes
2
replies
252
views
Variant Calling with Multiple Individuals in Freebayes
freebayes
variant-calling
updated 1 day ago by
size_t
▴ 60 • written 3 days ago by
Laurence
• 0
1
vote
4
replies
352
views
Log2 FC Threshold
GEO2R
updated 2 days ago by
Mensur Dlakic
★ 23k • written 4 days ago by
leenkhoury282
• 0
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
256
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
2
votes
2
replies
234
views
Cellranger count with error information "... which wasn't expected, or isn't valid in this context"
count
cellranger
scRNAseq
3 days ago by
diqixiaoyaoer
▴ 10
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
2
votes
1
reply
509
views
How to combine the outputs of repeat annotation softwares
RepeatProteinMasker
TRF
RepeatMasker
RepeatModeler
updated 2 days ago by
zijian
• 0 • written 21 months ago by
boymin2020
▴ 70
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
6
votes
10
replies
3.8k
views
Tool:
Giant Virus Finder - discover giant virus sequences in metagenomes
Giant-Virus-Finder
updated 3 days ago by
Ram
38k • written 7.1 years ago by
Csaba Kerepesi
▴ 350
3
votes
2
replies
229
views
How to make cut off linein cluster,
dendogram
Cutoff
R
updated 3 days ago by
GenoMax
127k • written 4 days ago by
Info.shi
▴ 30
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
5
votes
3
replies
256
views
Read lengths greater than insert length
NGS
updated 4 days ago by
GenoMax
127k • written 4 days ago by
shpak.max
▴ 30
1
vote
2
replies
264
views
How to get fraction of unspliced reads for specific gene from scRNAseq Cell Ranger output
scRNA-seq
python
CellRanger
updated 4 days ago by
Rob
5.9k • written 4 days ago by
codezero
• 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
2
votes
3
replies
363
views
Matching gene-expression data with clinical data: best practices.
best-practices
TCGA
updated 4 days ago by
Ram
38k • written 5 days ago by
jose.sgomez94
• 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
2
votes
7
replies
3.5k
views
error in downloading of some accesions with fastq-dump
fastq-dump
updated 4 days ago by
Utpal
• 0 • written 9 months ago by
pavelasquezv
▴ 50
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
3
votes
2
replies
4.2k
views
Problem running interproscan-5.15-54.0 for protein sequences
Interproscan
updated 4 days ago by
Pratyay
• 0 • written 7.4 years ago by
yangyongzhi2008
▴ 40
0
votes
2
replies
329
views
Understanding multifactor designs and control variables in DESeq2
RNA-seq
DESeq2
1 day ago by
kldsajf;ldsj;l
• 0
2
votes
4
replies
398
views
Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
analysis
DGE
3 days ago by
Adaline.D
• 0
2
votes
1
reply
228
views
Cellranger sequencing
normalization
scrnaseq
cellranger
updated 5 days ago by
ATpoint
70k • written 5 days ago by
crx6xw
▴ 10
1
vote
1
reply
224
views
Assembly at lineage level from shotgun data ?
fungus
MAGs
assembly
lineage
2 days ago by
v.berriosfarias
▴ 90
4
votes
6
replies
476
views
Python formatting when visualizing Primer3-py dimers
dictionary
primer3-py
python
5 days ago by
bhumm
▴ 40
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
4
replies
280
views
samtools fixmate: what's wrong with the terminal?
samtools
fixmate
updated 5 days ago by
Ram
38k • written 5 days ago by
npavliukovec
• 0
2
votes
1
reply
232
views
multiallelic variants
vcf
plink
updated 5 days ago by
raphael.B
▴ 310 • written 5 days ago by
Mali
• 0
1,000 results • Page
3 of 20
Recent Votes
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
Answer: What is the NCBI's definition of an "atypical genome"?
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?
Answer: Somatic truth set
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Answer: Align miRNA library (small RNA-seq) without trimming
by
Ming Tommy Tang
★ 2.9k
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
by
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 …
Answer: PTM-aware protein folding / docking
by
Mensur Dlakic
★ 23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
Answer: Admixture cv error
by
Declan
• 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…
Comment: Kallisto bustools for scRNA-seq
by
dsull
★ 4.0k
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…
Comment: Aberrant splicing in bulk RNAseq
by
dsull
★ 4.0k
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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by
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▴ 90
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…
Comment: Somatic truth set
by
lethalfang
▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata?
by
jv
★ 1.0k
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…
Comment: GO enrichment analysis
by
Jeremy
▴ 780
g:Profiler has an Arabidopsis option: [g:Profiler][1] [1]: https://biit.cs.ut.ee/gprofiler/gost
Answer: Any tips in landing a bioinformatic job?
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Carambakaracho
★ 3.2k
The first job is a nightmare and you will need some luck. I understand you're looking for an industry offering. Unfortunately I've worked o…
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