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46 results • Page
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4
votes
12
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4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 17 hours ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
0
votes
8
replies
280
views
Different output for read length
samtools
BAM
11 hours ago by
marco.barr
▴ 100
1
vote
7
replies
477
views
Question regarding WGCNA
WGCNA
Network-construction
17 hours ago by
deepak
• 0
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 20 hours ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
0
votes
5
replies
370
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 15 hours ago by
Jeremy Leipzig
22k • written 2 days ago by
schmince
• 0
2
votes
5
replies
240
views
Importing a fastq file
Fastq
updated 5 hours ago by
size_t
▴ 120 • written 1 day ago by
oumo
• 0
2
votes
4
replies
281
views
RNA seq analysis
DESeq
RNA-seq
updated 13 hours ago by
s.ghazala
• 0 • written 1 day ago by
prifa
▴ 10
0
votes
3
replies
197
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 18 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
Matthew
• 0
1
vote
3
replies
150
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 21 hours ago by
Pierre Lindenbaum
161k • written 21 hours ago by
ScottDansk
▴ 10
4
votes
3
replies
1.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 20 hours ago by
Pierre Lindenbaum
161k • written 22 hours ago by
Lila M
★ 1.2k
0
votes
3
replies
677
views
Pluritest for pluripotency broken
pluripotent
pluritest
cells
stem
updated 23 hours ago by
DGTool
• 0 • written 21 months ago by
yassine
• 0
0
votes
3
replies
464
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 17 hours ago by
Ram
43k • written 11 weeks ago by
maplewj
▴ 10
0
votes
3
replies
142
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
updated 17 hours ago by
Ram
43k • written 19 hours ago by
feather-W
• 0
1
vote
3
replies
194
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 15 hours ago by
GenoMax
142k • written 1 day ago by
cput
• 0
1
vote
3
replies
436
views
cellranger error message
multiplexing
cellranger
updated 13 hours ago by
Max
• 0 • written 12 weeks ago by
Alivia
▴ 10
1
vote
3
replies
291
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 12 hours ago by
bk11
★ 2.4k • written 5 days ago by
Yoosef
▴ 60
3
votes
3
replies
411
views
absolute path for symbolic links in Snakefile
Snakemake
updated 10 hours ago by
Jesse
▴ 770 • written 20 days ago by
yifangt86
▴ 60
0
votes
3
replies
199
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
updated 6 hours ago by
Philipp Bayer
8.4k • written 1 day ago by
rackbersingh
• 0
5
votes
2
replies
80
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 2 hours ago by
Gordon Smyth
★ 7.1k • written 5 hours ago by
gBioStar5
▴ 10
0
votes
2
replies
216
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 22 hours ago by
i.sudbery
19k • written 1 day ago by
Prawesh
• 0
0
votes
2
replies
153
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 20 hours ago by
Michael
54k • written 1 day ago by
ashaneev07
▴ 20
0
votes
2
replies
45
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
1 hour ago by
jain72744
▴ 10
0
votes
2
replies
121
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 14 hours ago by
GenoMax
142k • written 16 hours ago by
sainavyav22
• 0
0
votes
1
reply
97
views
Truncated metadata file report from ENA Portal API
ena
python
updated 11 hours ago by
GenoMax
142k • written 16 hours ago by
Giulia
• 0
0
votes
1
reply
89
views
input file for alternative splicing in rmats in linux
rmats
updated 16 hours ago by
Ram
43k • written 19 hours ago by
Lambodarswain316
• 0
0
votes
1
reply
52
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated just now by
ATpoint
82k • written 3 hours ago by
Amr
▴ 160
1
vote
1
reply
395
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 21 hours ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
0
votes
1
reply
49
views
DESeq2 error
DESeq2
updated 1 hour ago by
ATpoint
82k • written 5 hours ago by
sooni
▴ 20
0
votes
1
reply
268
views
Snakemake fails to find conda in PBS
snakemake
updated 15 hours ago by
tim.booth
▴ 60 • written 27 days ago by
yixinzeng
• 0
1
vote
0
replies
85
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
22 hours ago by
Shae
▴ 10
0
votes
0
replies
21
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
3 hours ago by
jain72744
▴ 10
0
votes
0
replies
23
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
3 hours ago by
singcell
• 0
0
votes
0
replies
11
views
Forum:
input file in rmats
rmats
1 hour ago by
Lambodarswain316
• 0
1
vote
0
replies
171
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
16 hours ago by
eebloom
▴ 80
0
votes
0
replies
60
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
16 hours ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
46
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
8 hours ago by
Aytaç
• 0
0
votes
0
replies
98
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
22 hours ago by
Javier
• 0
0
votes
0
replies
14
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
1 hour ago by
Samantha
• 0
2
votes
0
replies
54
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
13 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
57
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization
Mendelian
two-sample
12 hours ago by
Nikki
• 0
0
votes
0
replies
92
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
22 hours ago by
Zeng Hao
▴ 40
0
votes
0
replies
52
views
supervised admixture
supervised
admixture
11 hours ago by
RT
▴ 10
0
votes
0
replies
53
views
How do I calculate SE or P value if I only have BETA
prscsx
se
pvalue
beta
10 hours ago by
curious_butterfly
• 0
0
votes
0
replies
12
views
Microbial Signal Transduction Database
MiST
1 hour ago by
Shravani
• 0
0
votes
0
replies
44
views
Question about methylation location
Methylation
WGBS
bisulfide
8 hours ago by
Eren
• 0
0
votes
0
replies
1
view
bbduk.sh and seal.sh don't find my pattern
pattern
bbduk
java
bbmap
fastq
just now by
Assa Yeroslaviz
★ 1.8k
46 results • Page
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Recent Votes
use firehose_get to download TCGA data
Download data from TCGA
Comment: Importing a fastq file
EdgeR - relationship between logFC and coefficients
Answer: EdgeR - relationship between logFC and coefficients
Detecting highly variable genes within replicates
Detecting highly variable genes within replicates
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Amr
▴ 160
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rpolicastro
13k
Popular Question
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singcell
• 0
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Gordon Smyth
★ 7.1k
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anithanagaraj93
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Recent Replies
Comment: LncRNA Nomenclature
by
jain72744
▴ 10
My data is based on gene counts and the respective gene IDs are given so I should work with ENSGs? lncRNA_transcripts <- getBM(attributes …
Answer: DESeq2 error
by
ATpoint
82k
At least one group needs replication. That is the short answer. For a longer answer add details on experimental design.
Comment: When should I use R-MarkDown over R-Script ?
by
ATpoint
82k
Why particular question? Rmarkdown is a composite of markdown and code. You can nicely separate free text, explanation, comments etc. from…
Comment: LncRNA Nomenclature
by
ATpoint
82k
RNA-seq is typically analyzed on gene rather than transcript level. Are your counts gene or transcript?
Comment: EdgeR - relationship between logFC and coefficients
by
gBioStar5
▴ 10
Thanks a lot, this was very helpful. I'll keep that in mind.
Answer: EdgeR - relationship between logFC and coefficients
by
Gordon Smyth
★ 7.1k
Results presented by topTags() are on the log2 scale. Coefficients stored internally in the DGELRT object are on the loge scale. If you con…
Answer: Importing a fastq file
by
size_t
▴ 120
run command `explorer.exe .` in wsl terminal, and then drag file to folder
Comment: Contig assembly task, errors
by
Philipp Bayer
8.4k
Hi Ricardo! CAP3 is an 'older' overlap assembler from 1999 which is perfectly suited for these kinds of 'small' tasks. I used it last in my…
Comment: absolute path for symbolic links in Snakefile
by
Jesse
▴ 770
That's really handy, and much more of a general solution than stripping off the directory names! So yifangt86, if you're on Linux you can …
Comment: Truncated metadata file report from ENA Portal API
by
GenoMax
142k
Are you missing a `"` at the end of the URL. Doing wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
Comment: Different output for read length
by
marco.barr
▴ 100
very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
Comment: Different output for read length
by
Pierre Lindenbaum
161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
bk11
★ 2.4k
Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length
by
marco.barr
▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
Comment: Different output for read length
by
marco.barr
▴ 100
I just published my link on paste, why can't I see my public paste on the site?
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