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187 results • Page
4 of 4
Sort: Rank
Rank
Views
Votes
Replies
1
vote
3
replies
248
views
STAR aligner error
RNA-seq
STAR
slurm
updated 6 days ago by
Ram
43k • written 7 days ago by
M.
▴ 30
0
votes
2
replies
208
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
6 days ago by
Nicholas
• 0
0
votes
7
replies
504
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 6 days ago by
Wayne
★ 2.0k • written 8 days ago by
JACKY
▴ 140
0
votes
2
replies
222
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
ahmad.sajad4541
• 0
1
vote
9
replies
371
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 4 days ago by
i.sudbery
19k • written 7 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
4
replies
289
views
Correlation Analysis
statistics
methylation
NGS
expression
3 days ago by
Researcher
▴ 30
1
vote
5
replies
359
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 6 days ago by
Michael
54k • written 7 days ago by
qwertyuiop26
• 0
0
votes
1
reply
141
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 1 day ago by
Ram
43k • written 8 days ago by
David
• 0
0
votes
0
replies
106
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
5 days ago by
Javier
• 0
1
vote
7
replies
521
views
Question regarding WGCNA
WGCNA
Network-construction
5 days ago by
deepak
• 0
0
votes
3
replies
339
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
1 day ago by
mropri
▴ 150
3
votes
6
replies
479
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 2 days ago by
Pine
▴ 20 • written 9 days ago by
snajafy
• 0
2
votes
3
replies
323
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 5 days ago by
bk11
★ 2.4k • written 9 days ago by
Yoosef
▴ 60
0
votes
2
replies
262
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 4 days ago by
GenoMax
142k • written 11 days ago by
Ximena
• 0
0
votes
2
replies
291
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 11 days ago by
yahn
• 0
13
votes
14
replies
883
views
High Malat-1 expression in single cell data
single-cell
updated 6 days ago by
t.montserrat.ayuso
▴ 40 • written 15 days ago by
carolofharvest
▴ 40
4
votes
7
replies
383
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
1 day ago by
Chen
• 0
3
votes
3
replies
256
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 1 day ago by
Ram
43k • written 14 days ago by
Adyasha
• 0
0
votes
7
replies
407
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 1 day ago by
Mohamed Abderrahmane
▴ 20 • written 15 days ago by
matteo.levorato
• 0
0
votes
0
replies
111
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 1 day ago by
Ram
43k • written 15 days ago by
atharvakarkare14
▴ 30
3
votes
3
replies
430
views
absolute path for symbolic links in Snakefile
Snakemake
updated 5 days ago by
Jesse
▴ 770 • written 25 days ago by
yifangt86
▴ 60
0
votes
0
replies
178
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
1 day ago by
Emily
▴ 20
1
vote
2
replies
432
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
6 days ago by
Zeng Hao
▴ 40
1
vote
4
replies
403
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 4 days ago by
GenoMax
142k • written 27 days ago by
aniigodwinn
• 0
1
vote
0
replies
175
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
5 days ago by
eebloom
▴ 80
2
votes
3
replies
267
views
Finding variants within a subset of a BAM file
variant
calling
11 hours ago by
ramiro.barrantes
• 0
1
vote
4
replies
489
views
cellranger error message
multiplexing
cellranger
updated 4 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 5 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
3 days ago by
vytarasov
▴ 180
0
votes
3
replies
685
views
Pluritest for pluripotency broken
pluripotent
pluritest
cells
stem
updated 5 days ago by
DGTool
• 0 • written 21 months ago by
yassine
• 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 6 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 1 day ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 1 day ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 1 day ago by
Thind amarinder
▴ 340 • written 4.9 years ago by
garbuzov
▴ 70
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS
insertion site
trangene
de-novo
soap
updated 6 days ago by
Cameron.walker9900
• 0 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 4 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 2 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
187 results • Page
4 of 4
Recent Votes
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
Genome Visualization Tools
Answer: Genome Visualization Tools
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▴ 10
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Recent Replies
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R
by
jen
▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
Mensur Dlakic
★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools
by
dlera.lozano
▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat
by
Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Answer: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Trivas
★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R
by
jared.andrews07
★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran
by
GenoMax
142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content
by
noodle
▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file?
by
wyuan37
• 0
Hi, I emailed them and did get the bed file! Thank you so much.
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