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185 results • Page
2 of 4
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
214
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 2 days ago by
Michael
54k • written 3 days ago by
ashaneev07
▴ 20
1
vote
1
reply
434
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 2 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
4
votes
3
replies
2.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 2 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Lila M
★ 1.2k
2
votes
3
replies
201
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
ScottDansk
▴ 10
1
vote
0
replies
128
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
3 days ago by
Shae
▴ 10
0
votes
1
reply
179
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 3 days ago by
marco.barr
▴ 100 • written 3 days ago by
odi
▴ 10
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 2 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
1
vote
1
reply
139
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 3 days ago by
andres.firrincieli
3.6k • written 3 days ago by
kacollier
▴ 30
1
vote
2
replies
1.6k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 3 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
0
votes
0
replies
110
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 3 days ago by
Ram
43k • written 3 days ago by
curious_butterfly
• 0
0
votes
0
replies
113
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
3 days ago by
Zeng Hao
▴ 40
1
vote
4
replies
292
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
1 day ago by
rackbersingh
• 0
1
vote
3
replies
228
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 2 days ago by
GenoMax
142k • written 3 days ago by
cput
• 0
0
votes
0
replies
114
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
3 days ago by
asalimih
▴ 60
0
votes
2
replies
239
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
Prawesh
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 3 days ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
0
votes
1
reply
166
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 3 days ago by
marco.barr
▴ 100 • written 3 days ago by
elisheva
▴ 120
0
votes
0
replies
100
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 3 days ago by
Ram
43k • written 3 days ago by
mathavanbioinfo
▴ 90
1
vote
1
reply
261
views
Seurat V5 integration
Seurat
integration
updated 3 days ago by
Ram
43k • written 7 days ago by
starswillfade
▴ 10
0
votes
2
replies
217
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 3 days ago by
Ram
43k • written 4 days ago by
Sumeet
• 0
0
votes
0
replies
117
views
News:
Online course: Introduction to Deep Learning
Python
Deep-Learning
Convolutional-Neural-Network
Machine-Learning
updated 3 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 3 days ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
0
votes
2
replies
151
views
How/where can I get fungal mitogenome data for analysis?
fungal
mitogenome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
madders73
• 0
4
votes
2
replies
253
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
3 days ago by
mnx0723
• 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 3 days ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
3
votes
5
replies
341
views
RNA seq analysis
DESeq
RNA-seq
1 day ago by
prifa
▴ 10
10
votes
3
replies
300
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 3 days ago by
b.contreras.moreira
▴ 180 • written 4 days ago by
ijarne
• 0
0
votes
0
replies
141
views
Chance for trained without experience
bio
updated 3 days ago by
ATpoint
82k • written 3 days ago by
shehab
• 0
1
vote
2
replies
186
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
3 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
116
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
4 days ago by
Omics data mining
▴ 260
0
votes
2
replies
167
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
3 days ago by
njornet
▴ 20
0
votes
2
replies
196
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 3 days ago by
Adam
▴ 30 • written 4 days ago by
Darya
• 0
0
votes
5
replies
238
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 3 days ago by
Joe
21k • written 4 days ago by
Lemonhope
• 0
0
votes
0
replies
167
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
3 days ago by
Winter
• 0
0
votes
5
replies
287
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
3 days ago by
me
• 0
2
votes
1
reply
131
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
4 days ago by
analyst
▴ 50
0
votes
0
replies
86
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
4 days ago by
analyst
▴ 50
0
votes
0
replies
82
views
Blog:
Introduction to The Complete Sequence of a Human Genome
biotech
4 days ago by
usa.cd.genomics
• 0
0
votes
0
replies
88
views
Blog:
Overview of Nanopore Sequencing
biotech
4 days ago by
usa.cd.genomics
• 0
0
votes
0
replies
102
views
meffil.snp.concordance
meffil
methylation
snp_concordance
4 days ago by
kyj222637
• 0
0
votes
1
reply
145
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 3 days ago by
Bastien Hervé
5.3k • written 4 days ago by
sooni
▴ 20
1
vote
5
replies
413
views
HCL database download
HCL
updated 4 days ago by
Ram
43k • written 8 days ago by
sooni
▴ 20
0
votes
1
reply
245
views
barcode of TCR-sequencing
barcode
updated 4 days ago by
mizraelson
▴ 60 • written 11 days ago by
yueli7
▴ 250
0
votes
3
replies
226
views
STAR aligner error
RNA-seq
STAR
slurm
updated 3 days ago by
Ram
43k • written 4 days ago by
M.
▴ 30
0
votes
0
replies
95
views
monocle 3-- Could not get node in small cluster
monocle3
4 days ago by
synat.keam
▴ 100
0
votes
2
replies
195
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
3 days ago by
Nicholas
• 0
1
vote
4
replies
365
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
4 days ago by
heelpPlease
• 0
0
votes
7
replies
474
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 3 days ago by
Wayne
★ 2.0k • written 5 days ago by
JACKY
▴ 140
0
votes
0
replies
110
views
News:
Online course. -Time series analysis and Forecasting in R
Time-Series
Forecasting
R
Stastics
4 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
464
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 4 days ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
185 results • Page
2 of 4
Recent Votes
Gff To Vcf
Comment: Longest transcript variant per gene
Comment: Longest transcript variant per gene
Answer: Longest transcript variant per gene
Answer: Longest transcript variant per gene
Comment: Longest transcript variant per gene
Comment: Longest transcript variant per gene
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Recent Replies
Comment: Tissue-specific DEG analysis with DEseq2
by
ATpoint
82k
Sounds like full confounding. Be careful. Personally I would not do this comparison. There is no way to distinguish tissue effect from dono…
Answer: input file in rmats
by
Mathew
▴ 90
Hi, In the example they give in their GitHub (https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/README.md): They have 2 sample groups wi…
Comment: Longest transcript variant per gene
by
Mathew
▴ 90
I'm glad it worked well for you! Good luck with the rest of your project. I wish you the best.
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thanks so much
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Hello again, It works very well, thank you very much for this solution.
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Hello Mathew, Thanks for your answer, I'll try it and come back.
Answer: Longest transcript variant per gene
by
Mathew
▴ 90
Hi, why not write code to extract the longest variant? I copied these two in a txt file called "input.txt", and made three dummy variants …
Comment: Longest transcript variant per gene
by
GenoMax
142k
https://www.biostars.org/p/107759/<br> https://www.biostars.org/p/403649/ <!-- this is it -->
Answer: Kraken2 database
by
Mathew
▴ 90
Sorry, what analysis are you trying to perform with these databases? Based on your question, it appears you are using Kraken2 and Bracken.…
Comment: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
by
Mathew
▴ 90
I looked up a publication using CIBERSORT to see how they got the package, and indeed they acquired it through official website application…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
fracarb8
★ 1.6k
If you are using R, you should check the liana R implementation (https://github.com/saezlab/liana).
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Thank you Pierre, I am going to take some time to get my head around this and report back if it works.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Thanks for the crosspost! Just trying to get things figured out.
Answer: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
by
ATpoint
82k
To the best of my knowledge, CIBERSORT is and has always and only been available via the official website application from Stanford. Whatev…
Comment: BioLabDonkey - new Mac program for molecular biologists
by
vytarasov
▴ 180
Update of BioLabDonkey - Version 5.6 - In silico PCR function is added.
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