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27 results • Page
1 of 1
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0
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77
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
57 minutes ago by
Lila M
★ 1.2k
0
votes
0
replies
18
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
1 hour ago by
Shae
• 0
0
votes
1
reply
51
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 3 hours ago by
andres.firrincieli
3.6k • written 3 hours ago by
kacollier
▴ 30
0
votes
0
replies
40
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
variant
5 hours ago by
ashaneev07
▴ 20
0
votes
0
replies
50
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 7 hours ago by
Ram
43k • written 7 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
88
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
294
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
14 hours ago by
schmince
• 0
0
votes
2
replies
130
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 40 minutes 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 14 hours ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
0
votes
0
replies
60
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 13 hours ago by
Ram
43k • written 17 hours ago by
mathavanbioinfo
▴ 90
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
210
views
RNA seq analysis
DESeq
RNA-seq
updated 14 hours ago by
Ram
43k • written 22 hours ago by
prifa
• 0
0
votes
0
replies
106
views
Chance for trained without experience
bio
updated 23 hours ago by
ATpoint
82k • written 23 hours ago by
shehab
• 0
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
165
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 17 hours ago by
Adam
▴ 30 • written 1 day ago by
Darya
• 0
0
votes
5
replies
204
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
1
reply
126
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 19 hours ago by
Bastien Hervé
5.3k • written 1 day ago by
sooni
▴ 20
0
votes
3
replies
200
views
STAR aligner error
RNA-seq
STAR
slurm
updated 14 hours ago by
Ram
43k • written 1 day ago by
M.
▴ 30
0
votes
2
replies
186
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
19 hours ago by
Nicholas
• 0
0
votes
2
replies
194
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 17 hours ago by
swbarnes2
14k • written 1 day ago by
ahmad.sajad4541
• 0
0
votes
2
replies
146
views
Correlation Analysis
statistics
methylation
NGS
expression
2 hours ago by
Researcher
▴ 30
0
votes
0
replies
94
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
42 minutes ago by
Javier
• 0
1
vote
7
replies
468
views
Question regarding WGCNA
WGCNA
Network-construction
updated 14 hours ago by
Ram
43k • written 5 days ago by
deepak
• 0
1
vote
2
replies
202
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
2 hours ago by
Yoosef
▴ 60
27 results • Page
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Recent Votes
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?
Answer: How can I analyze normalized expression data?
Answer: Pruning Phylogenetic Trees and Bootstrap Values
Difference between Pysam Pileup and Fetch
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Popular Question
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Gordon Smyth
★ 7.1k
Popular Question
to
kacollier
▴ 30
Popular Question
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rackbersingh
• 0
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DKA
▴ 40
Centurion
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mathavanbioinfo
▴ 90
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graeme.thorn
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Recent Replies
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
▴ 90
from the documentation it seems that it reports limits for the value of log2 fold-change in an absolute sense. FCcutoff: Cut-off for…
Answer: 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
▴ 90
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_min…
Comment: Importing a fastq file
by
ATpoint
82k
Windows is mounted as `/mnt/c/...` in WSL (at least in WSL2).
Answer: Importing a fastq file
by
marco.barr
▴ 90
Can you explain better what you mean? If I understand correctly, your fastq file must be in the Ubuntu home folder of your wsl to be able t…
Answer: Seurat CellCycleScoring – confused about the proper order of operations when usi
by
Li
• 0
I‘m not an expert in sctransform or cellcyclescoring. But I think it's because sctransform creates a new assay named "SCT", which is differ…
Comment: How can I analyze normalized expression data?
by
mnx0723
• 0
thank you for comment
Comment: Pruning Phylogenetic Trees and Bootstrap Values
by
Zeng Hao
▴ 40
Dear Klaus, Thank you for the reply. If I could clarify with an example: With this tree, B0----------------- A -| B1----------…
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