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13,491 results • Page
1 of 270
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0
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0
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7
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
27 minutes ago by
Samantha
• 0
0
votes
0
replies
7
views
Microbial Signal Transduction Database
MiST
42 minutes ago by
Shravani
• 0
0
votes
0
replies
6
views
Forum:
input file in rmats
rmats
40 minutes ago by
Lambodarswain316
• 0
0
votes
1
reply
44
views
DESeq2 error
DESeq2
updated 50 minutes ago by
ATpoint
82k • written 4 hours ago by
sooni
▴ 20
0
votes
0
replies
19
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
2 hours ago by
singcell
• 0
0
votes
1
reply
38
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 51 minutes ago by
ATpoint
82k • written 2 hours ago by
Amr
▴ 160
0
votes
2
replies
34
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
10 minutes ago by
jain72744
▴ 10
0
votes
0
replies
18
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
2 hours ago by
jain72744
▴ 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
5
votes
2
replies
75
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 2 hours ago by
Gordon Smyth
★ 7.1k • written 4 hours ago by
gBioStar5
▴ 10
2
votes
5
replies
233
views
Importing a fastq file
Fastq
updated 4 hours ago by
size_t
▴ 120 • written 1 day ago by
oumo
• 0
0
votes
0
replies
43
views
Question about methylation location
Methylation
WGBS
bisulfide
7 hours ago by
Eren
• 0
0
votes
0
replies
44
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
51
views
How do I calculate SE or P value if I only have BETA
prscsx
se
pvalue
beta
9 hours ago by
curious_butterfly
• 0
0
votes
0
replies
51
views
supervised admixture
supervised
admixture
10 hours ago by
RT
▴ 10
0
votes
0
replies
56
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization
Mendelian
two-sample
11 hours ago by
Nikki
• 0
2
votes
0
replies
53
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
12 hours ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
277
views
Different output for read length
samtools
BAM
10 hours ago by
marco.barr
▴ 100
0
votes
1
reply
267
views
Snakemake fails to find conda in PBS
snakemake
updated 14 hours ago by
tim.booth
▴ 60 • written 27 days ago by
yixinzeng
• 0
0
votes
2
replies
120
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 13 hours ago by
GenoMax
142k • written 15 hours ago by
sainavyav22
• 0
0
votes
1
reply
95
views
Truncated metadata file report from ENA Portal API
ena
python
updated 10 hours ago by
GenoMax
142k • written 15 hours ago by
Giulia
• 0
0
votes
0
replies
58
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
15 hours ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
463
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 16 hours ago by
Ram
43k • written 11 weeks ago by
maplewj
▴ 10
0
votes
3
replies
141
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
updated 16 hours ago by
Ram
43k • written 18 hours ago by
feather-W
• 0
0
votes
3
replies
195
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 17 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
Matthew
• 0
0
votes
1
reply
88
views
input file for alternative splicing in rmats in linux
rmats
updated 15 hours ago by
Ram
43k • written 18 hours ago by
Lambodarswain316
• 0
0
votes
2
replies
152
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 19 hours ago by
Michael
54k • written 1 day ago by
ashaneev07
▴ 20
1
vote
1
reply
394
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 20 hours ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 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 19 hours ago by
Pierre Lindenbaum
161k • written 21 hours ago by
Lila M
★ 1.2k
1
vote
3
replies
148
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 20 hours ago by
Pierre Lindenbaum
161k • written 20 hours ago by
ScottDansk
▴ 10
1
vote
0
replies
84
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
21 hours ago by
Shae
▴ 10
0
votes
1
reply
145
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 23 hours ago by
marco.barr
▴ 100 • written 1 day ago by
odi
▴ 10
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 19 hours ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
1
vote
1
reply
111
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 23 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
kacollier
▴ 30
1
vote
2
replies
1.5k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 1 day ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
0
votes
0
replies
87
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 1 day ago by
Ram
43k • written 1 day ago by
curious_butterfly
• 0
0
votes
0
replies
91
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
21 hours ago by
Zeng Hao
▴ 40
0
votes
3
replies
196
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
updated 5 hours ago by
Philipp Bayer
8.4k • written 1 day ago by
rackbersingh
• 0
1
vote
3
replies
192
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 14 hours ago by
GenoMax
142k • written 1 day ago by
cput
• 0
0
votes
0
replies
96
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
1 day ago by
asalimih
▴ 60
0
votes
5
replies
368
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 14 hours ago by
Jeremy Leipzig
22k • written 2 days ago by
schmince
• 0
0
votes
2
replies
215
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 21 hours ago by
i.sudbery
19k • written 1 day ago by
Prawesh
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 1 day ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
0
votes
1
reply
153
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 1 day ago by
marco.barr
▴ 100 • written 1 day ago by
elisheva
▴ 120
0
votes
0
replies
88
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 1 day ago by
Ram
43k • written 1 day ago by
mathavanbioinfo
▴ 90
1
vote
1
reply
245
views
Seurat V5 integration
Seurat
integration
updated 1 day ago by
Ram
43k • written 4 days ago by
starswillfade
▴ 10
0
votes
2
replies
199
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 1 day ago by
Ram
43k • written 1 day ago by
Sumeet
• 0
0
votes
0
replies
109
views
News:
Online course: Introduction to Deep Learning
Python
Deep-Learning
Convolutional-Neural-Network
Machine-Learning
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 1 day ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
0
votes
2
replies
144
views
How/where can I get fungal mitogenome data for analysis?
fungal
mitogenome
updated 1 day ago by
GenoMax
142k • written 1 day ago by
madders73
• 0
13,491 results • Page
1 of 270
Recent Votes
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
A: Detecting highly variable genes within replicates
How to set a threshold for coefficient of variation in RNA-seq?
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13k
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• 0
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★ 7.1k
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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
What is your motivation to ask? Add some context. Beyond that, always use Rmd unless you write package code.
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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