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184 results • Page
2 of 4
Sort: Votes
Rank
Views
Votes
Replies
1
vote
0
replies
97
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
4 days ago by
tomas4482
▴ 400
1
vote
2
replies
361
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
180
views
Duplicated sequence samtools
bowtie2
samtools
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Moinuddin
• 0
1
vote
3
replies
436
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
1
vote
4
replies
341
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 4 days ago by
Ram
43k • written 9 days ago by
samRayne
• 0
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 4 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
1
vote
1
reply
173
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 3 days ago by
ATpoint
82k • written 4 days ago by
Pegasus
▴ 100
1
vote
2
replies
269
views
How to interpret infinite odds ratio?
statistics
3 days ago by
Lukas
• 0
1
vote
1
reply
147
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 3 days ago by
Ram
43k • written 3 days ago by
kilcdincer
▴ 10
1
vote
4
replies
346
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 3 days ago by
Juke34
8.6k • written 4 days ago by
Vijith
▴ 30
1
vote
2
replies
208
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 2 days ago by
colindaven
6.4k • written 3 days ago by
mbrav005
• 0
1
vote
1
reply
222
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 2 days ago by
dariober
14k • written 4 days ago by
Holly
▴ 10
1
vote
5
replies
217
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
biology_inform
▴ 50
1
vote
3
replies
279
views
Using ggplotly in R
ggplot
ggplotly
updated 2 days ago by
jared.andrews07
★ 16k • written 3 days ago by
jen
▴ 10
1
vote
5
replies
800
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
1
vote
3
replies
204
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
1
vote
4
replies
287
views
Add stats to boxplot in R
stats
R
2 days ago by
Ghada
• 0
1
vote
2
replies
221
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
2 days ago by
MarcosCosta
• 0
1
vote
1
reply
237
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
2 days ago by
ramiro.barrantes
• 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
1
vote
5
replies
261
views
Annotating file using bcftools
annotation
plink
bcftools
1 day ago by
kl
▴ 10
1
vote
1
reply
159
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 1 day ago by
Ram
43k • written 1 day ago by
m90
▴ 30
1
vote
3
replies
272
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 1 day ago by
GenoMax
142k • written 4 days ago by
ohtang7
▴ 40
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
1
vote
1
reply
184
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 1 day ago by
Jordan M Eizenga
▴ 460 • written 11 days ago by
sarumonsus
▴ 10
1
vote
0
replies
106
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
1
vote
5
replies
254
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 1 day ago by
Ram
43k • written 1 day ago by
manuelmourato25
• 0
1
vote
1
reply
168
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 1 day ago by
Ram
43k • written 2 days ago by
dwpeng
▴ 10
1
vote
4
replies
239
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 1 day ago by
Ram
43k • written 2 days ago by
kuttibiotech2009
▴ 30
1
vote
1
reply
156
views
API kegg - IndexError: list index out of range
kegg
API
updated 1 day ago by
Nyksubuz
▴ 20 • written 1 day ago by
mirwa.zidi93
• 0
1
vote
14
replies
619
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
23 hours ago by
hophuquy0944
• 0
1
vote
5
replies
282
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 11 hours ago by
dthorbur
★ 2.0k • written 1 day ago by
BATMAN
• 0
1
vote
8
replies
401
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 1 hour ago by
Alex Reynolds
35k • written 4 days ago by
ntsopoul
▴ 60
0
votes
1
reply
162
views
consensus sequence calling
consensus
updated 4 days ago by
bk11
★ 2.5k • written 4 days ago by
Ghada
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 3 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
4
replies
267
views
Merge clusters in Seurat UMAP
seurat
umap
21 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
96
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
3 days ago by
brunofelicianodeomena
• 0
0
votes
0
replies
99
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Dude
• 0
0
votes
1
reply
146
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
3 days ago by
sansan_96
▴ 90
0
votes
0
replies
105
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
4 days ago by
atariw
▴ 10
0
votes
1
reply
157
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 4 days ago by
GenoMax
142k • written 5 days ago by
octpus616
▴ 100
0
votes
0
replies
74
views
constructing pangenome through psvcp
psvcp
pangenome
19 hours ago by
analyst
▴ 50
0
votes
5
replies
319
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
4 days ago by
SilhouetteQ
• 0
0
votes
2
replies
189
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
2 days ago by
melissa.joubert
• 0
0
votes
0
replies
86
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
2 days ago by
Transmitting Science communication
▴ 70
0
votes
0
replies
94
views
ReactomeGSA
ReactomeGSA
2 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
88
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
4 days ago by
JACKY
▴ 140
0
votes
1
reply
214
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 19 hours ago by
GenoMax
142k • written 1 day ago by
huxiangyulove
• 0
0
votes
1
reply
535
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 4 days ago by
aw7
▴ 300 • written 28 days ago by
abhishekghadge
• 0
0
votes
3
replies
164
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
2 days ago by
Esraa
• 0
184 results • Page
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Recent Replies
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
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
by
ntsopoul
▴ 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
by
GenoMax
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
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
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…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
Zhenyu Zhang
★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
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