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328 results • Page
1 of 7
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Votes
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0
votes
0
replies
15
views
Read count vs Depth
Depth
count
Bedtools
Read
45 minutes ago by
Mary
• 0
0
votes
1
reply
79
views
scRNA data analysis , how to compare pattern in multiple samples
R
Bioinformatics
scRNA
data
40 minutes ago by
Confused_human
▴ 20
0
votes
1
reply
73
views
absolute running error: Error in if (!is.na(res)) { : the condition has length > 1
ABSOLUTE
error
2 hours ago by
qiuting
• 0
0
votes
0
replies
52
views
cosinoRmixedeffect: an R package for mixed-effects cosinor models
interactionmodel
cosinor
mixedeffect
circadian
9 hours ago by
Agnia
• 0
2
votes
3
replies
165
views
Annotation Visualization IGV
igv
alignment
gff
annotation
visualization
updated 15 hours ago by
Pierre Lindenbaum
158k • written 15 hours ago by
awhale01
• 0
0
votes
1
reply
119
views
Curated model organism gene functional annotations
Interpro
C.elegans
GO-terms
updated 19 hours ago by
Ram
41k • written 20 hours ago by
ian.will
▴ 10
2
votes
4
replies
309
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
20 hours ago by
cucindarko51
• 0
0
votes
2
replies
154
views
Very low successfully assigned alignments with feature counts
featureCounts
RNA-seq
updated 18 hours ago by
Istvan Albert
99k • written 20 hours ago by
Manuel
• 0
0
votes
0
replies
77
views
ASEReadCounter output wrong number of coverage
ASEReadCounter
1 day ago by
junhuili
• 0
1
vote
1
reply
1.0k
views
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
RNAseq
updated 1 day ago by
charles.feigin
• 0 • written 6 weeks ago by
xinrantian
▴ 20
0
votes
0
replies
82
views
megablast taxonomy assign in blobtools
blobtools
1 day ago by
bs
• 0
0
votes
1
reply
147
views
Aligning sequences with multiple genetic codes!
genetic_codes
codon
MEGA11
alignment
updated 19 hours ago by
5heikki
11k • written 1 day ago by
George X.
• 0
0
votes
1
reply
147
views
Cell ranger multi for demultiplexing FB files and GEX files
cellranger
updated 19 hours ago by
Ram
41k • written 1 day ago by
Shloka
• 0
0
votes
1
reply
151
views
Software for Spatial Transcriptomic data [NanoString; Visium]?
NanoString
Visium
Spatial-Transcriptomics
10X
1 day ago by
LauferVA
3.8k
1
vote
1
reply
141
views
ANNOVAR Download Failing
ANNOVAR
updated 1 day ago by
Ram
41k • written 1 day ago by
tony
• 0
0
votes
1
reply
152
views
Sorted bam files are empty after sorting them from bam
bam
dna
updated 1 day ago by
Ram
41k • written 1 day ago by
mgranada3
▴ 30
0
votes
2
replies
204
views
Downsampling ATAC-seq BAM files
ATAC-seq
1 day ago by
Elise
• 0
0
votes
0
replies
92
views
spatial metabolomics, python
spatial-metabolomics
updated 1 day ago by
Ram
41k • written 1 day ago by
joha
▴ 10
1
vote
4
replies
217
views
Feasibility of Enrichment Analysis from RTqPCR results
GO
RT-qPCR
Enrichment-Analysis
updated 1 day ago by
GenoMax
136k • written 1 day ago by
Javier
• 0
0
votes
0
replies
108
views
WGCNA for different tissues
WGCNA
Worms
RNA-Seq
1 day ago by
kdca
• 0
0
votes
1
reply
171
views
Contrasts in R
contrasts
r
updated 1 day ago by
jv
★ 1.3k • written 1 day ago by
SGMS
▴ 130
0
votes
1
reply
492
views
How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes
MLST
phylogenetic
nanopre
updated 1 day ago by
Joe
21k • written 1 day ago by
Ralph
• 0
0
votes
1
reply
156
views
How to remove 3rd codon positions in a multiple sequence allignment?
i
updated 1 day ago by
Ram
41k • written 1 day ago by
francesco.degiglio
• 0
0
votes
0
replies
113
views
Classification ML model using different type of data
machine-learning
transcriptomics
R
python
biomarkers
1 day ago by
sil_bioinfo
▴ 40
0
votes
0
replies
101
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
2 days ago by
Saad Khan
▴ 420
0
votes
0
replies
95
views
Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
2 days ago by
Adrian
• 0
3
votes
1
reply
149
views
GEO dataset Microarray data analysis help
R
microarray
NCBI
GEO
updated 1 day ago by
Ram
41k • written 2 days ago by
Confused_human
▴ 20
0
votes
3
replies
203
views
Microarray batch correction method suggestions
microarray
batch-correction
updated 1 day ago by
Ram
41k • written 2 days ago by
Sumeet
• 0
0
votes
0
replies
94
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
2 days ago by
Clayton
• 0
0
votes
0
replies
99
views
Enzyme commission number in ncbi Gene database
enzyme-commission-number
updated 1 day ago by
Ram
41k • written 2 days ago by
Maatary
• 0
0
votes
1
reply
147
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 2 days ago by
Brian Bushnell
20k • written 2 days ago by
isMM
• 0
2
votes
4
replies
263
views
error when installing gistic2 using conda
conda
gistic2
updated 1 day ago by
Ram
41k • written 2 days ago by
luckyday1661
• 0
0
votes
0
replies
111
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 2 days ago by
Ram
41k • written 2 days ago by
boone5jones
• 0
0
votes
0
replies
94
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
2 days ago by
S
• 0
0
votes
2
replies
200
views
what should I do if I get a compromised sample of scRNA-seq data?
scRNA-seq
data
snRNA-seq
updated 2 days ago by
ATpoint
78k • written 2 days ago by
wangjb702
• 0
0
votes
0
replies
93
views
Comparing 16S rRNA (culture) sequences with metagenome
metagenome
shotgun
rRNA_culture
16S
updated 2 days ago by
Ram
41k • written 2 days ago by
aswin
• 0
0
votes
4
replies
268
views
Filling gaps in BAM file
bamtools
samtools
gene
bam
updated 1 day ago by
seidel
11k • written 2 days ago by
hemr3
• 0
0
votes
1
reply
145
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
2 days ago by
enriquesan
• 0
0
votes
0
replies
81
views
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
ATAC-seq
2 days ago by
cyril-cros
▴ 940
0
votes
1
reply
140
views
Microbial gene coverage from blast result
gene
coverage
2 days ago by
aanchal.yadav
• 0
0
votes
0
replies
87
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
2 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
100
views
Funannotate iprscan Creates empty file
funannotate
interproscan
fungus
annotation
2 days ago by
Umer
▴ 50
2
votes
2
replies
210
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
2 days ago by
hkarakurt
▴ 180
0
votes
4
replies
658
views
How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction?
genome
threader
1 day ago by
peanut
• 0
2
votes
5
replies
232
views
kallisto index build difference according to version
index
version
kallisto
updated 3 days ago by
dsull
★ 5.1k • written 3 days ago by
estilo
• 0
0
votes
2
replies
518
views
Understanding gene level copy number data from TCGAbiolinks
CNV
TCGA
updated 3 days ago by
Zhenyu Zhang
★ 1.1k • written 13 months ago by
billyK
• 0
1
vote
3
replies
336
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq
mapping
updated 3 days ago by
GenoMax
136k • written 3 days ago by
bkffadia
• 0
0
votes
0
replies
115
views
Should I perform eQTL colocalization for just one of eGenes at a time?
colocalization
coloc
eCaviar
eQTL
4 days ago by
maximal_life
▴ 20
4
votes
2
replies
272
views
KEGG DATABASE
DATABASE
KEGG
updated 1 day ago by
jv
★ 1.3k • written 4 days ago by
Sijjil
• 0
0
votes
1
reply
216
views
Issue with genetic QC sex check
plink
5 days ago by
kl
▴ 10
328 results • Page
1 of 7
Recent Votes
Error in y - mu : non-numeric argument to binary operator - linear regression loop
Answer: Multi-factor designs in DiffBind
Answer: Calculate GC content for entire chromosome
STAR ALIGNMENT
STAR ALIGNMENT
Best method for batch correction of three datasets
CITEseq tutorial
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Popular Question
to
g.persic1991
• 0
Teacher
to
colindaven
5.8k
Scholar
to
andres.firrincieli
3.5k
Popular Question
to
Jaykumar
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samreen.jasvi
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jared.andrews07
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Recent Replies
Answer: Multi-factor designs in DiffBind
by
g.persic1991
• 0
Hi ATpoint, thanks for your quick answer. So, If I understand correctly, in this condition and using DiffBind, I can't take into acco…
Answer: Multi-factor designs in DiffBind
by
ATpoint
78k
Read the error: `There must be at least two sample groups with at least three replicates.` Yet, you only have n=2 per group. See for ex…
Comment: absolute running error: Error in if (!is.na(res)) { : the condition has length >
by
qiuting
• 0
this is the error.log: Detected error in sample P01_1 Error message: the condition has length > 1 Where: if !is.na(res) { mode.tab[(i…
Comment: STAR ALIGNMENT
by
Hải Đăng
• 0
Sis, where are you currently working? How can I get in touch with you?
Answer: RNA-Seq Data Analysis Workshop (March 11 - 14, 2024 in Berlin, Germany)
by
David Langenberger
10k
We already have an incredible number of registrations for this time. If you still want to be there, then you should register soon!
Comment: scRNA data analysis , how to compare pattern in multiple samples
by
ATpoint
78k
Can you please ask a precise question rather than posting a wall of code? What is the main problem you have, what did you try? Did you foll…
Comment: vcftools
by
sevda
• 0
Hello, Thank you for your attention. It ran successfully and I got no errors or warnings but no new files were created.
Comment: Resolving over clustered NGS with Q-scores
by
sam.himes92
• 0
The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Ram
41k
OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
Given files `genes.bed` and `snps.bed`, you could do something like: ``` $ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
Answer: How to add exon annotations to genome annotation
by
alex.zaccaron
▴ 380
You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
Comment: Annotation Visualization IGV
by
Pierre Lindenbaum
158k
and you got answer that should be validate (green tick), or people asked you questions but got no answers.
Comment: Annotation Visualization IGV
by
awhale01
• 0
Correct I have asked those questions before.
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