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184 results • Page
3 of 4
Sort: Rank
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Views
Votes
Replies
0
votes
2
replies
179
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
3
replies
346
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
5
replies
269
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 4 days ago by
Philipp Bayer
8.5k • written 4 days ago by
林明德
• 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
2
votes
4
replies
225
views
Help with IGV abbreviation
igv
updated 3 days ago by
Ram
43k • written 4 days ago by
GeneC
• 0
0
votes
1
reply
161
views
How to process Bulk WES data?
WES
WGS
updated 4 days ago by
GenoMax
142k • written 4 days ago by
wyuan37
• 0
0
votes
1
reply
161
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 4 days ago by
GenoMax
142k • written 4 days ago by
cedric.blais
• 0
0
votes
2
replies
432
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
0
votes
1
reply
151
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 4 days ago by
Ram
43k • written 4 days ago by
eking28
• 0
2
votes
5
replies
494
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 3 days ago by
Ram
43k • written 9 days ago by
Prawesh
• 0
1
vote
3
replies
435
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
2
replies
269
views
How to interpret infinite odds ratio?
statistics
3 days ago by
Lukas
• 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
0
votes
0
replies
104
views
reference-free assembly error assessment tools
assembly
4 days ago by
lagartija
▴ 160
2
votes
4
replies
295
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
2 days ago by
Esraa
• 0
2
votes
0
replies
141
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
4 days ago by
Biostar
2.8k
0
votes
1
reply
142
views
Splitting Seurat object by sample layers
seurat
updated 4 days ago by
Ram
43k • written 4 days ago by
kilcdincer
▴ 10
0
votes
4
replies
258
views
Galaxy StringTie error
stringtie
galaxy
3 days ago by
trkfs
• 0
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
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
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
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
3
votes
2
replies
283
views
imputation through beagle
panel
beagle
reference
imputation
3 days ago by
analyst
▴ 50
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
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
3
votes
1
reply
216
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 4 days ago by
aw7
▴ 300 • written 9 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
103
views
Reference panel of normals for ensembl named refgenome
Mutect2
4 days ago by
gernophil
▴ 80
1
vote
0
replies
97
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
4 days ago by
tomas4482
▴ 400
2
votes
6
replies
387
views
BWA alignment
Samtools
bam
updated 2 days ago by
a.alnawfal.1992
▴ 260 • written 5 days ago by
Vahid
• 0
3
votes
2
replies
191
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
0
votes
1
reply
157
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 4 days ago by
Philipp Bayer
8.5k • written 5 days ago by
samRayne
• 0
0
votes
1
reply
247
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 4 days ago by
Ram
43k • written 8 days ago by
Nikki
• 0
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
196
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 4 days ago by
chrchang523
10k • written 9 days ago by
analyst
▴ 50
0
votes
0
replies
110
views
lncRNA
tcga
lncrna
5 days ago by
jain72744
▴ 10
0
votes
1
reply
243
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 8 days ago by
jain72744
▴ 10
2
votes
5
replies
571
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 5 days ago by
arctic
▴ 40 • written 14 days ago by
M.
▴ 30
1
vote
2
replies
360
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
2
votes
1
reply
263
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 5 days ago by
pjb39
▴ 210 • written 7 days ago by
beantkapoor16
▴ 10
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
8
replies
380
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
128
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
233
views
input file in rmats
rmats
updated 5 days ago by
Mathew
▴ 140 • written 7 days ago by
Lambodarswain316
• 0
3
votes
3
replies
363
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 4 days ago by
Mathew
▴ 140 • written 7 days ago by
Christopher
• 0
6
votes
7
replies
388
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
5 days ago by
sansan_96
▴ 90
2
votes
3
replies
282
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
2
votes
1
reply
234
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 6 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
melissachua90
▴ 70
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 6 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
0
votes
4
replies
405
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by
beginner123
• 0
184 results • Page
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How can I perform Differential expression analysis with just one control and one cancer sample?
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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
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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
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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
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…
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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 -…
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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