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89 results • Page
2 of 2
Sort: Views
Rank
Views
Votes
Replies
0
votes
2
replies
152
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
8 hours ago by
melissa.joubert
• 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
1
reply
150
views
input file for alternative splicing in rmats in linux
rmats
updated 6 days ago by
Ram
43k • written 6 days ago by
Lambodarswain316
• 0
0
votes
0
replies
141
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
5 days ago by
singcell
• 0
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
0
replies
137
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
6 days ago by
Shae
▴ 10
0
votes
1
reply
136
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 21 hours ago by
GenoMax
142k • written 22 hours ago by
bioinfo
▴ 150
1
vote
1
reply
126
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 22 hours ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
0
replies
120
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
6 days ago by
asalimih
▴ 60
0
votes
0
replies
116
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 6 days ago by
Ram
43k • written 6 days ago by
curious_butterfly
• 0
0
votes
0
replies
114
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 1 day ago by
Ram
43k • written 16 days ago by
atharvakarkare14
▴ 30
0
votes
1
reply
109
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
12 hours ago by
sansan_96
▴ 90
0
votes
0
replies
107
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 6 days ago by
Ram
43k • written 6 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
106
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
6 days ago by
Javier
• 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
0
votes
0
replies
102
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
0
votes
0
replies
101
views
reference-free assembly error assessment tools
assembly
1 day ago by
lagartija
▴ 160
0
votes
0
replies
99
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
2 days ago by
atariw
▴ 10
0
votes
0
replies
96
views
Reference panel of normals for ensembl named refgenome
Mutect2
2 days ago by
gernophil
▴ 80
0
votes
3
replies
95
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
5 hours ago by
Esraa
• 0
0
votes
0
replies
91
views
Is there a real ground truth for CNV data?
CNV
1 day ago by
jennyp0706
• 0
1
vote
0
replies
91
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
2 days ago by
tomas4482
▴ 400
0
votes
1
reply
91
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
updated 4 hours ago by
ATpoint
82k • written 6 hours ago by
egascon
• 0
0
votes
1
reply
90
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 3 hours ago by
Joe
21k • written 12 hours ago by
iqra
• 0
0
votes
0
replies
90
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
1 day ago by
ramiro.barrantes
• 0
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
1
reply
86
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 4 hours ago by
GenoMax
142k • written 10 hours ago by
chrisk
• 0
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
0
replies
81
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Bhavya
• 0
0
votes
0
replies
64
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 14 hours ago by
GenoMax
142k • written 15 hours ago by
Dude
• 0
0
votes
0
replies
60
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
15 hours ago by
brunofelicianodeomena
• 0
0
votes
0
replies
49
views
ReactomeGSA
ReactomeGSA
8 hours ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
42
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 2 hours ago by
ATpoint
82k • written 3 hours ago by
yura.grabovska
▴ 70
0
votes
0
replies
35
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
3 hours ago by
Lélé
• 0
0
votes
1
reply
24
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
30 minutes ago by
asalimih
▴ 60
0
votes
0
replies
18
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
1 hour ago by
jway
• 0
0
votes
0
replies
11
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
26 minutes ago by
diqixiaoyaoer
▴ 10
0
votes
0
replies
12
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
22 minutes ago by
ev97
▴ 20
0
votes
0
replies
5
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
6 minutes ago by
shpak.max
▴ 50
89 results • Page
2 of 2
Recent Votes
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
Answer: genome finishing
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Recent Awards •
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13k
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▴ 160
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nd48
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Recent Replies
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…
Answer: Cannot install bwa-mem2 via conda
by
Istvan Albert
100k
The problem is caused by running the ARM-based conda. Bioinformatics software is compiled for Intel based CPUs only. Uninstall that versio…
Comment: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
[https://www.biostars.org/p/9559284/][1] you could try this [1]: https://www.biostars.org/p/9559284/
Comment: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
it's also true that now I only have one pod5 folder, thanks anyway for clarifying the focus of the issue. Yes, they are probably secondary …
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
I'm unsure. I will say that looking for [ normalize](https://github.com/search?q=repo%3Atanaylab%2Fmetacells%20normalize&type=code) among t…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
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…
Answer: genome finishing
by
nd48
▴ 20
What is the input? Do you have short reads (e.g. illumina 100bp paired reads)? As mentioned already, you already have the consensus i.e. c…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
biology_inform
▴ 50
I've been exploring different visualization tools like Circos and shinyCircos, and I've noticed that they require an input file similar to …
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