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113,968 results • Page
1 of 2280
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
38
views
Resolving over clustered NGS with Q-scores
NGS
phred
Q-score
overclustering
49 minutes ago by
sam.himes92
• 0
1
vote
1
reply
98
views
Ambient RNA removal method that generates whole (integer) counts
pseudobulk
soupX
DESeq2
single-cell
updated 2 hours ago by
jared.andrews07
★ 16k • written 21 hours ago by
EK
• 0
0
votes
1
reply
53
views
Curated model organism gene functional annotations
Interpro
C.elegans
GO-terms
updated 2 hours ago by
Ram
41k • written 3 hours ago by
ian.will
▴ 10
1
vote
4
replies
253
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
3 hours ago by
cucindarko51
• 0
773
votes
164
replies
129k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
1
vote
10
replies
1.8k
views
Scanpy Pearson residual PCA error
python
scRNA
scanpy
PCA
updated 3 hours ago by
Maëlick
• 0 • written 15 months ago by
Emily
▴ 70
0
votes
0
replies
41
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
3 hours ago by
Ming Tommy Tang
★ 3.6k
0
votes
2
replies
70
views
Very low successfully assigned alignments with feature counts
featureCounts
RNA-seq
updated 1 hour ago by
Istvan Albert
99k • written 3 hours ago by
Manuel
• 0
0
votes
4
replies
196
views
Need help to find FASTA sequence from dbSNP
dbSNP
SNP
FASTA
updated 4 hours ago by
GenoMax
136k • written 10 hours ago by
syedahumairagillani
• 0
4
votes
5
replies
265
views
Calculate GC content for entire chromosome
bam
GC
assembly
bwa-mem
updated 2 hours ago by
colindaven
5.8k • written 1 day ago by
skilleta0527
• 0
3
votes
2
replies
128
views
Execute R command on specific termimal
R
updated 2 hours ago by
Ram
41k • written 7 hours ago by
QX
• 0
1
vote
1
reply
147
views
How to use Nextflow to call scripts from different environments?
anaconda
conda
nextflow
updated 2 hours ago by
Ram
41k • written 18 hours ago by
O.rka
▴ 710
0
votes
0
replies
54
views
ASEReadCounter output wrong number of coverage
ASEReadCounter
12 hours ago by
junhuili
• 0
1
vote
5
replies
806
views
Strandedness of RNA-seq results
dual-RNA-seq
featurecounts
strandedness
HISAT2
updated 11 hours ago by
charles.feigin
• 0 • written 18 months ago by
jamesymtang
▴ 10
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 11 hours ago by
charles.feigin
• 0 • written 6 weeks ago by
xinrantian
▴ 20
0
votes
0
replies
61
views
megablast taxonomy assign in blobtools
blobtools
15 hours ago by
bs
• 0
0
votes
1
reply
96
views
Aligning sequences with multiple genetic codes!
genetic_codes
codon
MEGA11
alignment
updated 2 hours ago by
5heikki
11k • written 18 hours ago by
George X.
• 0
0
votes
1
reply
119
views
Cell ranger multi for demultiplexing FB files and GEX files
cellranger
updated 2 hours ago by
Ram
41k • written 19 hours ago by
Shloka
• 0
0
votes
1
reply
119
views
Software for Spatial Transcriptomic data [NanoString; Visium]?
NanoString
Visium
Spatial-Transcriptomics
10X
16 hours ago by
LauferVA
3.8k
4
votes
15
replies
6.4k
views
8 follow
bbmap split paired-end reads back into separated fastq files?
genome
next-gen-sequencing
bbmap
alignment
updated 15 hours ago by
GenoMax
136k • written 5.2 years ago by
c.e.chong
▴ 60
0
votes
1
reply
135
views
AssemblyMAFFromAnchorWavePlugin IndexOutOfBoundsException
phg
updated 22 hours ago by
lcj34
▴ 250 • written 1 day ago by
ryan
• 0
1
vote
1
reply
116
views
ANNOVAR Download Failing
ANNOVAR
updated 21 hours ago by
Ram
41k • written 23 hours ago by
tony
• 0
0
votes
1
reply
124
views
Sorted bam files are empty after sorting them from bam
bam
dna
updated 21 hours ago by
Ram
41k • written 23 hours ago by
mgranada3
▴ 30
0
votes
2
replies
177
views
Downsampling ATAC-seq BAM files
ATAC-seq
19 hours ago by
Elise
• 0
0
votes
0
replies
72
views
spatial metabolomics, python
spatial-metabolomics
updated 1 day ago by
Ram
41k • written 1 day ago by
joha
▴ 10
0
votes
3
replies
311
views
RNA seq
Differential-gene-expression
updated 1 day ago by
jv
★ 1.3k • written 3 days ago by
Byonkesh
• 0
0
votes
4
replies
418
views
Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom
RNAseq
differential-gene-expession
limma
batch-effect
updated 1 day ago by
Ram
41k • written 5 days ago by
fluke
• 0
1
vote
4
replies
191
views
Feasibility of Enrichment Analysis from RTqPCR results
GO
RT-qPCR
Enrichment-Analysis
updated 11 hours ago by
GenoMax
136k • written 1 day ago by
Javier
• 0
0
votes
0
replies
87
views
WGCNA for different tissues
WGCNA
Worms
RNA-Seq
1 day ago by
kdca
• 0
0
votes
2
replies
168
views
Issues while running blastx
blastx
RNA-seq
updated 11 hours ago by
GenoMax
136k • written 1 day ago by
Foad
▴ 10
0
votes
1
reply
115
views
Tophat2 Error running 'long_spanning_reads' on M1 Mac
Tophat2
Boost
RiboSeq
M1-Mac
updated 1 day ago by
Ram
41k • written 1 day ago by
riboseq938
• 0
0
votes
1
reply
148
views
Contrasts in R
contrasts
r
updated 1 day ago by
jv
★ 1.3k • written 1 day ago by
SGMS
▴ 130
1
vote
5
replies
626
views
ATAC-Seq and RPKM
RPKM
ATAC-Seq
updated 1 day ago by
ATpoint
78k • written 9 weeks ago by
qudrat.nii
• 0
0
votes
1
reply
1.3k
views
Correlation RNA-seq and ATAC-seq
RNA-Seq
R
gene
updated 1 day ago by
Tao Zhu
▴ 10 • written 3.4 years ago by
pastel950818
• 0
5
votes
4
replies
859
views
Methods to integrate ATAC-seq and RNA-seq
RNA-seq
ATAC-seq
updated 1 day ago by
Tao Zhu
▴ 10 • written 4 months ago by
Chris
▴ 230
0
votes
1
reply
125
views
Issues with Chromosome Encoding and VCF Annotation in dbSNP Alpha Release
bcftools
dbSNP
tabix
vcf
updated 1 day ago by
Ram
41k • written 1 day ago by
Fernando
• 0
0
votes
1
reply
369
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
1
vote
2
replies
169
views
contrast file in DESeq2 bioconductor
DEseq2
updated 1 day ago by
Ram
41k • written 1 day ago by
r.shiasi3897
▴ 10
1
vote
2
replies
289
views
Best method for batch correction of three datasets
RNA-seq
updated 10 hours ago by
ATpoint
78k • written 1 day ago by
CTLong
▴ 20
0
votes
1
reply
133
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
93
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
83
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
1 day ago by
Saad Khan
▴ 420
0
votes
0
replies
79
views
Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
1 day ago by
Adrian
• 0
1
vote
7
replies
279
views
How to download multiple genome files using command line (MacOS) using datasets
ncbi-datasets
Bacteria
Genome
updated 22 hours ago by
Ram
41k • written 1 day ago by
scholaraspect2008
• 0
3
votes
1
reply
139
views
GEO dataset Microarray data analysis help
R
microarray
NCBI
GEO
updated 1 day ago by
Ram
41k • written 1 day ago by
Confused_human
▴ 20
0
votes
3
replies
188
views
Microarray batch correction method suggestions
microarray
batch-correction
updated 21 hours ago by
Ram
41k • written 1 day ago by
Sumeet
• 0
0
votes
0
replies
90
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
1 day ago by
Clayton
• 0
0
votes
0
replies
96
views
Enzyme commission number in ncbi Gene database
enzyme-commission-number
updated 1 day ago by
Ram
41k • written 1 day ago by
Maatary
• 0
2
votes
1
reply
168
views
Best way to normalize transcript reads data for PCA & correlation and further biostat analysis
transcript_reads
updated 1 day ago by
Jeremy
▴ 860 • written 1 day ago by
Faith
▴ 40
2
votes
2
replies
165
views
Help with gatk CreateSequenceDictionary
GATK
updated 1 day ago by
GenoMax
136k • written 1 day ago by
Chris
▴ 230
113,968 results • Page
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Answer: Ambient RNA removal method that generates whole (integer) counts
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Recent Replies
Comment: Resolving over clustered NGS with Q-scores
by
sam.himes92
• 0
Yes at 5%.
Comment: Resolving over clustered NGS with Q-scores
by
ATpoint
78k
Has phiX been spiked in to increase nucleotide diversity.
Comment: How is "integer score for display" calculated in MACS2
by
SplitInf
▴ 10
since this is one of the top search results, I'm cross-posting this comment from another user (alexbarrera) "that the values of the 5th co…
Comment: Very low successfully assigned alignments with feature counts
by
Istvan Albert
99k
Load up your data in IGV and visualize it relative to your annotation file. It will tell you where the data aligns. 5% match on a 99% ali…
Answer: Ambient RNA removal method that generates whole (integer) counts
by
jared.andrews07
★ 16k
I've definitely just rounded soupX output and had no issues with pseudobulking. A colleague speaks highly of Cellbender, though it take…
Comment: Curated model organism gene functional annotations
by
manaswwm
▴ 490
I thought Interproscan already has species-specific information, for example [this][1] page for Buchnera aphidicola. You can try to search …
Comment: Aligning sequences with multiple genetic codes!
by
5heikki
11k
I don't understand your problem. What do you mean when you write: > These genes even in the same species may use different genetic codes. …
Comment: An issue with gtf file (ballgownrsem)
by
cucindarko51
• 0
I also encountered issues when running ballgownrsem with gff files. Ballgown object was created, there is no informations about TPM and FPK…
Answer: Scanpy Pearson residual PCA error
by
Maëlick
• 0
I had the same problems and then realize that I forgot the preprocessing! If you add this commands before running the PCA, it should work:…
Comment: Calculate GC content for entire chromosome
by
colindaven
5.8k
Try tripling your example seq length, see 20bp min region -l INT min region length to output [20] To answer your question, it …
Comment: Very low successfully assigned alignments with feature counts
by
GenoMax
136k
Is the genome/annotation from the same source i.e. Ensembl or so it appears?
Comment: Calculate GC content for entire chromosome
by
ATpoint
78k
What does this do? It's not documented well and does not work for me in terms of, it produces no output: cat foo.fa >chr1 GCGC…
Comment: Need help to find FASTA sequence from dbSNP
by
GenoMax
136k
Did you not see the last part in my comment above about how to get the sequence?
Comment: Execute R command on specific termimal
by
QX
• 0
Hi @atpoint Thank you for your answer!
Comment: Need help to find FASTA sequence from dbSNP
by
syedahumairagillani
• 0
Thank you for your response. Actually I am looking for fasta sequence of SNP as I shared via image, rather than just location. Would you p…
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