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183 results • Page
2 of 4
Sort: replies
Rank
Views
Votes
Replies
2
votes
4
replies
294
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
2 days ago by
Esraa
• 0
2
votes
4
replies
269
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 2 days ago by
yura.grabovska
▴ 90 • written 2 days ago by
ev97
▴ 20
1
vote
4
replies
285
views
Add stats to boxplot in R
stats
R
2 days ago by
Ghada
• 0
1
vote
4
replies
282
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
2 days ago by
Arton
▴ 10
0
votes
4
replies
239
views
Sequencing Depth (Read Depth) Calculations
depth
1 day ago by
LucisTheFather
• 0
3
votes
4
replies
353
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Pierre Lindenbaum
161k
0
votes
4
replies
244
views
calculating genomic coverage/ base overlap in R
genomics
updated 1 day ago by
Ram
43k • written 2 days ago by
Xbox_27
• 0
1
vote
4
replies
230
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 23 hours ago by
Ram
43k • written 2 days ago by
kuttibiotech2009
▴ 30
0
votes
4
replies
264
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 17 hours ago by
Tony
• 0 • written 2 days ago by
vk
▴ 10
0
votes
4
replies
257
views
Merge clusters in Seurat UMAP
seurat
umap
14 hours ago by
kilcdincer
▴ 10
6
votes
4
replies
270
views
Details on salmon index
Salmon
updated 9 hours ago by
Rob
6.6k • written 1 day ago by
Lorenzo
• 0
3
votes
4
replies
270
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 7 hours ago by
Jeremy Leipzig
22k • written 1 day ago by
Ali
• 0
1
vote
3
replies
202
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 2 days ago by
shpak.max
▴ 50
2
votes
3
replies
219
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 23 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
0
votes
3
replies
260
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 3 days ago by
noodle
▴ 580 • written 3 days ago by
doramora
▴ 10
1
vote
3
replies
797
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 1 day ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
2
votes
3
replies
213
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 3 days ago by
Ram
43k • written 3 days ago by
Prawesh
• 0
1
vote
3
replies
270
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 1 day ago by
GenoMax
142k • written 3 days ago by
ohtang7
▴ 40
3
votes
3
replies
224
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 1 day ago by
ATpoint
82k • written 2 days ago by
Alexandra
• 0
3
votes
3
replies
362
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 3 days ago by
Mathew
▴ 140 • written 6 days ago by
Christopher
• 0
1
vote
3
replies
434
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
4 days ago by
kalavattam
▴ 190
3
votes
3
replies
189
views
getting exon coordinates
genomics
updated 1 day ago by
Ram
43k • written 1 day ago by
Xbox_27
• 0
0
votes
3
replies
192
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 4 days ago by
Ram
43k • written 4 days ago by
yau
• 0
0
votes
3
replies
202
views
How to access GWAVA software of data
GWAVA
updated 3 days ago by
GenoMax
142k • written 3 days ago by
nonaddldy
▴ 10
0
votes
3
replies
353
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
4 days ago by
mropri
▴ 150
0
votes
3
replies
211
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 3 days ago by
GenoMax
142k • written 3 days ago by
RNAseqer
▴ 270
0
votes
3
replies
232
views
Sam file Header problem
Sam
Header
problem
file
updated 15 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
saifulislam99121
• 0
3
votes
3
replies
268
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 4 days ago by
Ram
43k • written 17 days ago by
Adyasha
• 0
0
votes
3
replies
162
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
2 days ago by
Esraa
• 0
2
votes
3
replies
276
views
Finding variants within a subset of a BAM file
variant
calling
3 days ago by
ramiro.barrantes
• 0
2
votes
3
replies
280
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
4 days ago by
Azra
▴ 10
1
vote
3
replies
278
views
Using ggplotly in R
ggplot
ggplotly
updated 2 days ago by
jared.andrews07
★ 16k • written 3 days ago by
jen
▴ 10
0
votes
3
replies
202
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
updated 6 hours ago by
andres.firrincieli
3.6k • written 2 days ago by
mavy
▴ 10
0
votes
3
replies
344
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
2
replies
183
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 1 day ago by
Ram
43k • written 2 days ago by
jsmith120f
• 0
0
votes
2
replies
296
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 14 days ago by
yahn
• 0
0
votes
2
replies
177
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
3 days ago by
IdaHao0921
• 0
0
votes
2
replies
430
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
4 days ago by
David Langenberger
11k
1
vote
2
replies
359
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 4 days ago by
Ram
43k • written 5 days ago by
t.fortunato.asquini
• 0
1
vote
2
replies
179
views
Duplicated sequence samtools
bowtie2
samtools
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Moinuddin
• 0
1
vote
2
replies
216
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
2 days ago by
MarcosCosta
• 0
1
vote
2
replies
268
views
How to interpret infinite odds ratio?
statistics
3 days ago by
Lukas
• 0
0
votes
2
replies
295
views
How are score_weights calculated in this code?
single-cell
6 days ago by
carolofharvest
▴ 40
3
votes
2
replies
189
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 4 days ago by
ATpoint
82k • written 4 days ago by
jennyp0706
• 0
2
votes
2
replies
197
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 1 day ago by
Ram
43k • written 1 day ago by
txema.heredia
▴ 130
0
votes
2
replies
221
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
2 days ago by
Chen
• 0
0
votes
2
replies
210
views
Output file of samtools flagstat empty
samtools-flagstat
updated 4 days ago by
colindaven
6.4k • written 5 days ago by
ramendra.sarma
• 0
2
votes
2
replies
203
views
Genome Visualization Tools
bacterial
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
dlera.lozano
▴ 10
2
votes
2
replies
196
views
genome finishing
finishing
genome
updated 2 days ago by
nd48
▴ 20 • written 2 days ago by
trezini
• 0
1
vote
2
replies
206
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 2 days ago by
colindaven
6.4k • written 2 days ago by
mbrav005
• 0
183 results • Page
2 of 4
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Recent Replies
Answer: Design for complex RNA-Seq experiment using Deseq2
by
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This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
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▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool
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142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
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by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
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by
ashkan
▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
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▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
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Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
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hannes.bongartz
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It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
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43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
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I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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