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104,154 results • Page
1 of 2084
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Votes
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0
votes
1
reply
90
views
annovar DB download problem (hg38)
annovar
intevar
just now by
Chang Ki
• 0
0
votes
0
replies
9
views
Filter out reads with hidden tags in bam files
BAM
samtools
13 minutes ago by
jkim
▴ 110
0
votes
1
reply
57
views
Reference genome fasta file
genome
Reference
updated 36 minutes ago by
Dave Carlson
▴ 890 • written 4 hours ago by
synat.keam
▴ 50
0
votes
0
replies
8
views
How to extract coefficients corresponding to data from each time in a mixed effect model in R?
model
lmer
mixed-effect
33 minutes ago by
lzgcas
• 0
1
vote
1
reply
16
views
InterProScan, Conserved domain database, SMART and PFAM
InterProscan
SMART
and
PFAM
CDD
updated 24 minutes ago by
lieven.sterck
14k • written 53 minutes ago by
lukhanyomakhabane
▴ 30
0
votes
3
replies
79
views
Visualize coverage across exons with varying lengths
Exons
python
readdepth
binning
updated 1 hour ago by
Friederike
8.4k • written 8 hours ago by
Kash
▴ 90
0
votes
2
replies
23
views
Filtering data from snpEFF annotated file
Filtering
snpEff
annotation
1 hour ago by
maajid
• 0
1
vote
2
replies
49
views
DEXSeq unable to find an inherited method for function ‘NSBS’ for signature ‘"CompressedIntegerList"’
DEXSeq
R
Bioconductor
just now by
ta_awwad
▴ 320
0
votes
0
replies
18
views
Change colors of each histogram in correlation and phenotypic distribution plot
Histogram
2 hours ago by
waqaskhokhar999
▴ 130
0
votes
0
replies
16
views
PyGNA
PyGNA
network
analysis
geneset
2 hours ago by
melissachua90
▴ 40
0
votes
0
replies
24
views
detectRUNS R package error
mapping
detectRUNS
R
ROH
homozygosity
3 hours ago by
Roisin
• 0
689
votes
160
replies
93k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 4 months ago by
Biostar
970 • written 5.7 years ago by
Istvan Albert
94k
0
votes
0
replies
27
views
Regression - when to include interaction term?
covariate
interaction
regression
statistics
2 hours ago by
Beqy
• 0
0
votes
0
replies
23
views
Intergrated list of pathogenic bacterial and fungal species
fungi
pathogen
bacteria
metagenome
3 hours ago by
bioinfo_ga
▴ 50
7
votes
6
replies
695
views
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
aspera
ascp
updated 21 minutes ago by
GenoMax
119k • written 7 weeks ago by
ATpoint
64k
0
votes
2
replies
46
views
-bash: indexdb_rna: command not found
sortmerna
miniconda
linux
conda
fasta
1 hour ago by
Dude
• 0
0
votes
0
replies
40
views
Is there a python package that can replicate this model?
python
R
data
analysis
statsmodels
4 hours ago by
Mike
▴ 10
0
votes
0
replies
26
views
SOAPdenovo2 error
execution
soapdenovo2
error
4 hours ago by
Shakunthala Natarajan
• 0
0
votes
0
replies
31
views
How to Configure Blat server in Cyverse
gf
dedicated
Cyverse
BLAT
server
3 hours ago by
sabreenaalam12345
• 0
0
votes
1
reply
48
views
mapped paired end reads extraction from .bam file
reads
mapped
samtools
updated 5 hours ago by
Pierre Lindenbaum
148k • written 6 hours ago by
tehreemali
• 0
0
votes
0
replies
27
views
peptide sequence (already know protein ID ) to domain match
peptide
domain
structure
sequence
protein
5 hours ago by
16622080827
• 0
0
votes
1
reply
48
views
Merge 2 imputation reference panels
panel
Reference
Imputation
updated 3 hours ago by
4galaxy77
2.2k • written 6 hours ago by
GiantSilverSoy
▴ 90
2
votes
0
replies
31
views
Is there any difference between analyzing the WES and WGS data via GATK best practice?
WGS
GATK
WES
6 hours ago by
Mohamad
▴ 20
1
vote
6
replies
107
views
How to extra read pair orientation from paired end reads
hi-c
alignment
samtools
3 hours ago by
Zhang Yun
• 0
3
votes
9
replies
4.5k
views
ValueError: invalid literal for int() with base 10: 'start' computeMatrix of deeptools
ChIP-Seq
Deeptools
updated 7 hours ago by
ronaldgevern
• 0 • written 5.2 years ago by
salamandra
▴ 500
2
votes
1
reply
119
views
Mapping GeneSymbol plus cDNA position to a Chr:Position ... without transcript ID.
annotation
splice
site
transcript
build
updated 6 hours ago by
Mark
★ 1.1k • written 10 hours ago by
Vincent Laufer
★ 2.2k
0
votes
0
replies
61
views
Diffbind not calling sites as differentially bound
DiffBind
12 hours ago by
ipsc-jl
• 0
0
votes
0
replies
61
views
FastStructure allele frequency output did not make sense
plink
frequency
faststructure
allele
13 hours ago by
yanni.ccy11
• 0
1
vote
1
reply
103
views
VST in DESeq2 giving negative values
DESeq2
R
Bioconductor
updated 15 hours ago by
ATpoint
64k • written 17 hours ago by
sanatbhadsavle
• 0
0
votes
0
replies
66
views
ADMIXTURE zsh:abort error
error
population
Admixture
structure
genetics
15 hours ago by
Clovering
▴ 20
3
votes
2
replies
121
views
Relative log expression normalization without negative values
rna-seq
updated 15 hours ago by
ATpoint
64k • written 16 hours ago by
demoraesdiogo2017
▴ 70
7
votes
7
replies
4.3k
views
6 follow
Get BUSCO gene descriptions
BUSCO
de novo assembly
updated 15 hours ago by
Ram
36k • written 6.4 years ago by
pbigbig
▴ 230
3
votes
2
replies
101
views
Parsing VEP tab-delimited output (the "Extra" column)
tab
vep
17 hours ago by
Ram
36k
0
votes
2
replies
71
views
Correlogram under barplot
ggplot2
R
visualization
updated 1 hour ago by
Friederike
8.4k • written 17 hours ago by
LChart
630
0
votes
0
replies
64
views
deeptools kmeans heatmap
diffbind
deeptools
kmeans
ATAC
clustering
updated 18 hours ago by
GenoMax
119k • written 18 hours ago by
rekharichardson
• 0
0
votes
0
replies
51
views
CalibrateDragstrModel - Not enough cases to estimate parameters, using defaults
dragen-os
calibration
gatk
dragen
alignment
18 hours ago by
Nemo
• 0
0
votes
1
reply
72
views
other.columns = 'gIsWellAboveBG' is not being added to the object
R
Agilent
updated 19 hours ago by
Kevin Blighe
82k • written 20 hours ago by
Fate
• 0
1
vote
4
replies
138
views
lasso-penalised model and glm to identify best predictors genes.
lasso-penalised
glm
DESeq2
model
R
3 hours ago by
Georges
• 0
2
votes
1
reply
81
views
How to merge 3 tsv files in R? with the same columns names ?
R
tsv
updated 19 hours ago by
LChart
630 • written 20 hours ago by
Amr
▴ 20
0
votes
1
reply
68
views
Validate RNAseq reads against array genotypes?
rnaseq
sequencing
contamination
array
genotyping
updated 19 hours ago by
LChart
630 • written 20 hours ago by
S
• 0
1
vote
3
replies
555
views
Memory Issue while doing single cell seq analysis
LR
interaction
analysis
scrna
scran-seq
updated 19 hours ago by
4galaxy77
2.2k • written 13 months ago by
cogen859
• 0
0
votes
0
replies
52
views
Tool:
CZ CELLxGENE - Single-cell visualization and analysis tool
scRNA-seq
rnaseq
visualization
tool
20 hours ago by
mczerwinski
• 0
0
votes
0
replies
49
views
How to download Affymetrix SNP 6.0 level 1 data from TCGA?
6.0
TCGA
SNP
Affymetrix
21 hours ago by
lishujin
• 0
0
votes
0
replies
80
views
Job:
Bioinformatics programming with HIV Databases, Los Alamos National Lab
programmer
job
updated 20 hours ago by
4galaxy77
2.2k • written 21 hours ago by
btf
▴ 10
2
votes
1
reply
108
views
How to adjust y-axis scale on scanpy scatter plot
scRNA
seq
scanpy
data
RNA
updated 20 hours ago by
Wayne
★ 1.3k • written 1 day ago by
Emily
▴ 20
0
votes
5
replies
201
views
Blastp issue - "No alias or index file found for protein database"
blast
transdecoder
bash
updated 14 hours ago by
GenoMax
119k • written 22 hours ago by
Corey
• 0
2
votes
2
replies
110
views
Unix - help with ls command
ls
command
mkdir
unix
updated 22 hours ago by
Ram
36k • written 22 hours ago by
kaelie.nelson
• 0
2
votes
5
replies
170
views
phylip format sequence name/header issue
phylogentics
7 hours ago by
hafiz.talhamalik
▴ 340
0
votes
0
replies
52
views
problem about snpflip
snpflip
1 day ago by
dongxinyu510
• 0
1
vote
0
replies
75
views
Herald:
The Biostar Herald for Monday, August 15, 2022
herald
1 day ago by
Biostar
970
104,154 results • Page
1 of 2084
Recent Votes
Comment: InterProScan, Conserved domain database, SMART and PFAM
A: extract and generate a VCF file with only "PASS"
Comment: DEXSeq unable to find an inherited method for function ‘NSBS’ for signature ‘"C
Do you know where to find the isolation source of all bacteria?
Answer: Do you know where to find the isolation source of all bacteria?
Comment: Setting up Aspera Connect (ascp) on Linux and macOS
Answer: Unix - help with ls command
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Recent Replies
Comment: InterProScan, Conserved domain database, SMART and PFAM
by
lieven.sterck
14k
it is very well likely that Interproscan uses different thresholds (compared to what the individual DBs do) which could indeed result in do…
Answer: Reference genome fasta file
by
Dave Carlson
▴ 890
What tool are you using for your RNA-Seq alignment/mapping? That choice will determine whether you need to use the transcriptome fasta fil…
Comment: DEXSeq unable to find an inherited method for function ‘NSBS’ for signature ‘"C
by
ta_awwad
▴ 320
Hi Alex, thanks for your reply. > class (se) [1] "RangedSummarizedExperiment" attr(,"package") [1] "SummarizedExperiment"
Comment: DEXSeq unable to find an inherited method for function ‘NSBS’ for signature ‘"C
by
ATpoint
64k
`class(se)`?
Comment: Correlogram under barplot
by
Friederike
8.4k
It's not entirely clear to me what the issue is. Your toy example seems to give you what you want. Where's the hold up?
Answer: Visualize coverage across exons with varying lengths
by
Friederike
8.4k
deepTools' `computeMatrix` and `plotProfile` may do what you need. You'd need a BED file of exons and a bigWig file of read coverages, thou…
Comment: Filtering data from snpEFF annotated file
by
maajid
• 0
Sir , here I just want to filter out exonic variants .
Comment: Filtering data from snpEFF annotated file
by
Pierre Lindenbaum
148k
duplicate of your previous question : https://www.biostars.org/p/9534057/
Comment: -bash: indexdb_rna: command not found
by
Dude
• 0
uhhhh.... I see, thank you so much!!
Comment: Setting up Aspera Connect (ascp) on Linux and macOS
by
GenoMax
119k
If you don't have access to the folder on the server (you likely have write only access) email NCBI SRA help desk and let them know. They s…
Comment: -bash: indexdb_rna: command not found
by
Arup Ghosh
3.0k
The `indexdb_rna` binary has been removed from version 4.0. https://github.com/biocore/sortmerna/wiki/User-manual-v4.0#Usage
Comment: Evaluate normalization method for scRNA-Seq Dataset
by
spriyansh29
▴ 30
Hi @lchart, thanks for your response. I believe I was not clear on my part in explaining the problem. I did go through the publication, as …
Comment: Finding out if a query sequence is present in a read library / bam file (blast a
by
chronotope
▴ 10
Here is the command I run (still not a looped one, just wanted to test calling the .jar from elsewhere and that already breaks) `java -jar…
Comment: Finding out if a query sequence is present in a read library / bam file (blast a
by
chronotope
▴ 10
Hi, I am having trouble making a loop for this command - when I run a singular instance from the ../jvarkit directory, it runs smooth, but …
Comment: lasso-penalised model and glm to identify best predictors genes.
by
Georges
• 0
Thanks @lchart I tuned `lambda` to higher values and got less number of parameters (genes). However, processing more thank 4 ~ 5 genes in …
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