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Limit : this year
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13,000 results • Page
2 of 260
Sort: Rank
Rank
Views
Votes
Replies
0
votes
1
reply
167
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Chen
• 0
1
vote
1
reply
164
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Pegasus
▴ 100
0
votes
1
reply
125
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 20 hours ago by
Ram
43k • written 1 day ago by
Emily
▴ 20
1
vote
1
reply
172
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 1 day ago by
zx8754
11k • written 1 day ago by
ohtang7
▴ 40
0
votes
0
replies
89
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
1 day ago by
Spring
• 0
0
votes
2
replies
169
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
1 day ago by
IdaHao0921
• 0
0
votes
3
replies
331
views
Snakemake wrapper issue
fastqc
snakemake
updated 1 day ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
5
replies
251
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 1 day ago by
Philipp Bayer
8.5k • written 1 day 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 20 hours ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
199
views
Help with IGV abbreviation
igv
updated 20 hours ago by
Ram
43k • written 1 day ago by
GeneC
• 0
0
votes
1
reply
155
views
How to process Bulk WES data?
WES
WGS
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
0
votes
1
reply
150
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 1 day ago by
GenoMax
142k • written 1 day ago by
cedric.blais
• 0
0
votes
2
replies
418
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
1 day ago by
David Langenberger
11k
0
votes
1
reply
141
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 1 day ago by
Ram
43k • written 1 day ago by
eking28
• 0
1
vote
5
replies
470
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 20 hours ago by
Ram
43k • written 6 days ago by
Prawesh
• 0
1
vote
3
replies
418
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
1 day ago by
kalavattam
▴ 190
1
vote
2
replies
256
views
How to interpret infinite odds ratio?
statistics
1 day ago by
Lukas
• 0
1
vote
2
replies
167
views
Duplicated sequence samtools
bowtie2
samtools
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Moinuddin
• 0
0
votes
0
replies
101
views
reference-free assembly error assessment tools
assembly
2 days ago by
lagartija
▴ 160
2
votes
4
replies
273
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
10 hours ago by
Esraa
• 0
2
votes
0
replies
135
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
2 days ago by
Biostar
2.8k
0
votes
1
reply
134
views
Splitting Seurat object by sample layers
seurat
updated 1 day ago by
Ram
43k • written 2 days ago by
kilcdincer
▴ 10
0
votes
4
replies
238
views
Galaxy StringTie error
stringtie
galaxy
1 day ago by
trkfs
• 0
0
votes
0
replies
99
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
2 days ago by
atariw
▴ 10
0
votes
1
reply
145
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 2 days ago by
GenoMax
142k • written 2 days ago by
octpus616
▴ 100
1
vote
4
replies
328
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 16 hours ago by
Juke34
8.6k • written 2 days ago by
Vijith
▴ 30
0
votes
1
reply
154
views
consensus sequence calling
consensus
updated 2 days ago by
bk11
★ 2.4k • written 2 days ago by
Ghada
• 0
0
votes
3
replies
179
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 1 day ago by
Ram
43k • written 2 days ago by
yau
• 0
3
votes
2
replies
261
views
imputation through beagle
panel
beagle
reference
imputation
1 day ago by
analyst
▴ 50
0
votes
0
replies
85
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
2 days ago by
JACKY
▴ 140
0
votes
1
reply
510
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 2 days ago by
aw7
▴ 300 • written 25 days ago by
abhishekghadge
• 0
3
votes
1
reply
205
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 2 days ago by
aw7
▴ 300 • written 6 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
97
views
Reference panel of normals for ensembl named refgenome
Mutect2
2 days ago by
gernophil
▴ 80
1
vote
0
replies
91
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
2 days ago by
tomas4482
▴ 400
2
votes
6
replies
359
views
BWA alignment
Samtools
bam
updated 12 hours ago by
a.alnawfal.1992
▴ 260 • written 2 days ago by
Vahid
• 0
3
votes
2
replies
180
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 2 days ago by
ATpoint
82k • written 2 days ago by
jennyp0706
• 0
0
votes
1
reply
154
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 2 days ago by
Philipp Bayer
8.5k • written 3 days ago by
samRayne
• 0
0
votes
1
reply
237
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 1 day ago by
Ram
43k • written 5 days ago by
Nikki
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
186
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 2 days ago by
chrchang523
10k • written 7 days ago by
analyst
▴ 50
0
votes
0
replies
104
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
0
votes
1
reply
232
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 5 days ago by
jain72744
▴ 10
2
votes
5
replies
552
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 3 days ago by
arctic
▴ 40 • written 12 days ago by
M.
▴ 30
1
vote
2
replies
346
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 2 days ago by
Ram
43k • written 3 days ago by
t.fortunato.asquini
• 0
2
votes
1
reply
248
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 3 days ago by
pjb39
▴ 210 • written 5 days ago by
beantkapoor16
▴ 10
0
votes
2
replies
200
views
Output file of samtools flagstat empty
samtools-flagstat
updated 2 days ago by
colindaven
6.4k • written 3 days ago by
ramendra.sarma
• 0
0
votes
0
replies
105
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
3 days ago by
BioinfGuru
★ 1.7k
2
votes
8
replies
348
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
121
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
3 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
226
views
input file in rmats
rmats
updated 3 days ago by
Mathew
▴ 140 • written 5 days ago by
Lambodarswain316
• 0
13,000 results • Page
2 of 260
Recent Votes
Answer: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
Answer: Cannot install bwa-mem2 via conda
Answer: Sub-sampling a BAM to a fixed number of reads
Comment: Downsample BAM file to specific amount of reads
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
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Recent Replies
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
• 0
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R
by
jared.andrews07
★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
If you only have supplementary alignments then they may be caused by reasons mentioned here --> https://www.biostars.org/p/308853/ I did no…
Comment: Cannot install bwa-mem2 via conda
by
Pierre Lindenbaum
161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
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