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116,842 results • Page
1 of 2337
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1
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324
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ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated just now by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
0
votes
2
replies
111
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
just now by
Lila M
★ 1.2k
0
votes
3
replies
30
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 10 minutes ago by
Pierre Lindenbaum
161k • written 49 minutes ago by
ScottDansk
▴ 10
0
votes
0
replies
19
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
1 hour ago by
Shae
• 0
0
votes
1
reply
83
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 3 hours ago by
marco.barr
▴ 100 • written 12 hours ago by
odi
▴ 10
1
vote
4
replies
108
views
Importing a fastq file
Fastq
3 hours ago by
oumo
• 0
0
votes
6
replies
2.0k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated just now by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
795
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
1
vote
1
reply
56
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 3 hours ago by
andres.firrincieli
3.6k • written 4 hours ago by
kacollier
▴ 30
0
votes
0
replies
42
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 2 minutes ago by
Michael
54k • written 5 hours ago by
ashaneev07
▴ 20
1
vote
2
replies
1.4k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 7 hours ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
0
votes
0
replies
50
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 8 hours ago by
Ram
43k • written 8 hours ago by
curious_butterfly
• 0
0
votes
0
replies
55
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
1 hour ago by
Zeng Hao
▴ 40
0
votes
1
reply
97
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
updated 9 hours ago by
GenoMax
142k • written 11 hours ago by
rackbersingh
• 0
0
votes
1
reply
101
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 11 hours ago by
Pierre Lindenbaum
161k • written 12 hours ago by
Matthew
• 0
0
votes
1
reply
93
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 7 hours ago by
Ram
43k • written 12 hours ago by
cput
• 0
0
votes
0
replies
66
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
12 hours ago by
asalimih
▴ 60
0
votes
4
replies
296
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
14 hours ago by
schmince
• 0
0
votes
2
replies
134
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 1 hour ago by
i.sudbery
19k • written 14 hours ago by
Prawesh
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 15 hours ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
0
votes
1
reply
120
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 15 hours ago by
marco.barr
▴ 100 • written 18 hours ago by
elisheva
▴ 120
0
votes
0
replies
60
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 14 hours ago by
Ram
43k • written 17 hours ago by
mathavanbioinfo
▴ 90
0
votes
1
reply
212
views
Seurat V5 integration
Seurat
integration
updated 14 hours ago by
Ram
43k • written 4 days ago by
starswillfade
▴ 10
0
votes
2
replies
172
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 14 hours ago by
Ram
43k • written 1 day ago by
Sumeet
• 0
0
votes
0
replies
75
views
News:
Online course: Introduction to Deep Learning
Python
Deep-Learning
Convolutional-Neural-Network
Machine-Learning
updated 14 hours ago by
Ram
43k • written 18 hours ago by
carlopecoraro2
★ 2.5k
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 19 hours ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
0
votes
2
replies
117
views
How/where can I get fungal mitogenome data for analysis?
fungal
mitogenome
updated 19 hours ago by
GenoMax
142k • written 19 hours ago by
madders73
• 0
4
votes
2
replies
206
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
8 hours ago by
mnx0723
• 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 22 hours ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
0
votes
3
replies
211
views
RNA seq analysis
DESeq
RNA-seq
updated 15 hours ago by
Ram
43k • written 23 hours ago by
prifa
• 0
10
votes
3
replies
258
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 23 hours ago by
b.contreras.moreira
▴ 180 • written 1 day ago by
ijarne
• 0
0
votes
0
replies
106
views
Chance for trained without experience
bio
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
shehab
• 0
1
vote
2
replies
150
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
1 day ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
81
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
1 day ago by
Omics data mining
▴ 260
0
votes
2
replies
138
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
23 hours ago by
njornet
▴ 20
0
votes
2
replies
166
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 18 hours ago by
Adam
▴ 30 • written 1 day ago by
Darya
• 0
0
votes
5
replies
205
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 22 hours ago by
Joe
21k • written 1 day ago by
Lemonhope
• 0
0
votes
0
replies
120
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
3 hours ago by
Winter
• 0
0
votes
5
replies
251
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
20 hours ago by
me
• 0
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by
DGTool
• 0 • written 4.8 years ago by
ww22runner
▴ 60
2
votes
1
reply
110
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
1 day ago by
analyst
▴ 50
0
votes
0
replies
74
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
1 day ago by
analyst
▴ 50
0
votes
0
replies
72
views
Blog:
Introduction to The Complete Sequence of a Human Genome
biotech
1 day ago by
usa.cd.genomics
• 0
0
votes
0
replies
77
views
Blog:
Overview of Nanopore Sequencing
biotech
1 day ago by
usa.cd.genomics
• 0
0
votes
0
replies
88
views
meffil.snp.concordance
meffil
methylation
snp_concordance
1 day ago by
kyj222637
• 0
0
votes
1
reply
126
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 20 hours ago by
Bastien Hervé
5.3k • written 1 day ago by
sooni
▴ 20
1
vote
5
replies
392
views
HCL database download
HCL
updated 1 day ago by
Ram
43k • written 5 days ago by
sooni
▴ 20
0
votes
1
reply
239
views
barcode of TCR-sequencing
barcode
updated 1 day ago by
mizraelson
▴ 60 • written 8 days ago by
yueli7
▴ 250
0
votes
3
replies
205
views
STAR aligner error
RNA-seq
STAR
slurm
updated 15 hours ago by
Ram
43k • written 1 day ago by
M.
▴ 30
0
votes
0
replies
90
views
monocle 3-- Could not get node in small cluster
monocle3
1 day ago by
synat.keam
▴ 100
116,842 results • Page
1 of 2337
Recent Votes
Comment: Importing a fastq file
ComBat_Seq stuck adjusting the data
Comment: Conda severely broken after attempting mamba install
Comment: Problem with Seurat package in PercentageFeatureSet function
Answer: Can I merge Hi-C fastq files from different lanes?
A: How to get SNP identifiers from VCF file?
Answer: How can I analyze normalized expression data?
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Recent Replies
Answer: ComBat_Seq stuck adjusting the data
by
Jaïr
• 0
Same keeps happening to me; but it is weird, I corrected the batch effect with the same exact function a few months ago and worked fine. I …
Comment: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
by
Lila M
★ 1.2k
Thank you for the feedback! I already used just the `samtools fastq -1 R1.fq.gz -2 R2.fq.gz -s Rx.fq.gz -0 R0.fq.gz`. Could you please exp…
Comment: Nextflow: how to get the process work dir, within the process
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
by
Pierre Lindenbaum
161k
faster use samtools collate+ fastq samtools collate -uOn128 in.bam TMDIR | samtools fastq -1 R1.fq.gz -2 R2.fq.gz -s Rx.fq.gz -…
Comment: Nextflow: how to get the process work dir, within the process
by
ScottDansk
▴ 10
legend thank you so much!
Answer: Nextflow: how to get the process work dir, within the process
by
Pierre Lindenbaum
161k
``` écho \${PWD} ``` <!-- where is Brian Brian is in the kitchen -->
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
i.sudbery
19k
What is the output of `samtools flagstat`?
Comment: Pluritest for pluripotency broken
by
DGTool
• 0
Hi, just a question, were you able to find a way to get it to work locally? My understanding from looking around seems to be at least so fa…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
Yoosef
▴ 60
Thanks a lot for your response. Today, I finally understood what my problem was. I have used CreateAssayObject function, while I should ha…
Comment: Correlation Analysis
by
Researcher
▴ 30
there is only one value of methylation and expression per gene. I did perform corr(gene_corr$methylation_values, gene_corr$expression_value…
Answer: Enhanced Volcano-Cut off
by
marco.barr
▴ 100
from the documentation it seems that it reports limits for the value of log2 fold-change in an absolute sense. FCcutoff: Cut-off for…
Comment: Importing a fastq file
by
oumo
• 0
The fastq file is in my local disk, and I want to upload it to Ubuntu
Comment: Conda severely broken after attempting mamba install
by
andres.firrincieli
3.6k
I have been there... I just reinstalled conda.
Comment: Importing a fastq file
by
marco.barr
▴ 100
That's right.. With `cp` command from terminal cp /mnt/c/path/to/your/fastq/file.fastq /path/in/wsl/
Comment: Copy number Variation analysis using conumee
by
zylcc2
• 0
if your seqnames include "chrX" or "chrY", should add "chrXY=TRUE". like this : `anno_combine <- CNV.create_anno(bin_minprobes = 15, bin_mi…
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