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181 results • Page
1 of 4
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Views
Votes
Replies
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
1 day ago by
vytarasov
▴ 180
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 5 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 180
10
votes
14
replies
682
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 5 days ago by
GenoMax
142k • written 11 days ago by
nicole.kavanagh
• 0
13
votes
14
replies
841
views
High Malat-1 expression in single cell data
single-cell
updated 4 days ago by
t.montserrat.ayuso
▴ 40 • written 13 days ago by
carolofharvest
▴ 40
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 2 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
2
votes
12
replies
2.8k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 4 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
4
votes
12
replies
4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 3 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
0
votes
11
replies
427
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
10 hours ago by
Tuck898
• 0
1
vote
10
replies
868
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 6 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
1
vote
9
replies
348
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 2 days ago by
i.sudbery
19k • written 5 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 4 days ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
2
votes
8
replies
267
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 15 hours ago by
Pierre Lindenbaum
161k • written 18 hours ago by
Matteo Ungaro
▴ 100
3
votes
8
replies
543
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
6 days ago by
Qroid
▴ 40
3
votes
8
replies
630
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 6 days ago by
Chris Dean
▴ 410 • written 10 days ago by
sovrappensiero
▴ 100
0
votes
8
replies
407
views
Different output for read length
samtools
BAM
3 days ago by
marco.barr
▴ 100
1
vote
7
replies
495
views
Question regarding WGCNA
WGCNA
Network-construction
3 days ago by
deepak
• 0
0
votes
7
replies
478
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 4 days ago by
Wayne
★ 2.0k • written 6 days ago by
JACKY
▴ 140
6
votes
7
replies
287
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
9 hours ago by
sansan_96
▴ 90
9
votes
7
replies
7.1k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 1 day ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
1
vote
7
replies
548
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 2 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
schmince
• 0
0
votes
6
replies
329
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
updated 11 hours ago by
Pierre Lindenbaum
161k • written 2 days ago by
ajbarrett98
• 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 4 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 6 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 3 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
3
votes
6
replies
442
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 5 hours ago by
Pine
▴ 20 • written 7 days ago by
snajafy
• 0
1
vote
6
replies
695
views
anRichment is missing
WGCNA
anRichment
updated 6 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
1
vote
5
replies
454
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 11 hours ago by
arctic
▴ 40 • written 9 days ago by
M.
▴ 30
3
votes
5
replies
343
views
RNA seq analysis
DESeq
RNA-seq
2 days ago by
prifa
▴ 10
0
votes
5
replies
264
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
2 days ago by
SilhouetteQ
• 0
0
votes
5
replies
241
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 4 days ago by
Joe
21k • written 4 days ago by
Lemonhope
• 0
2
votes
5
replies
364
views
Importing a fastq file
Fastq
updated 3 days ago by
size_t
▴ 120 • written 3 days ago by
oumo
• 0
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 4 days ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
1
vote
5
replies
338
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 4 days ago by
Michael
54k • written 5 days ago by
qwertyuiop26
• 0
1
vote
5
replies
325
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 6 days ago by
Ram
43k • written 6 days ago by
snajafy
• 0
5
votes
5
replies
282
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
5 days ago by
Chris
▴ 280
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS
insertion site
trangene
de-novo
soap
updated 4 days ago by
Cameron.walker9900
• 0 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
5
replies
291
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
4 days ago by
me
• 0
1
vote
5
replies
415
views
HCL database download
HCL
updated 5 days ago by
Ram
43k • written 9 days ago by
sooni
▴ 20
0
votes
5
replies
254
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
2 hours ago by
feather-W
• 0
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 16 hours ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 4 days ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
1
vote
4
replies
482
views
cellranger error message
multiplexing
cellranger
updated 2 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
3
votes
4
replies
430
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 6 days ago by
Gordon Smyth
★ 7.1k • written 9 days ago by
SHN
▴ 40
1
vote
4
replies
365
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
5 days ago by
heelpPlease
• 0
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 1 day ago by
Ruqaiya
• 0 • written 6.4 years ago by
dllopezr
▴ 130
1
vote
4
replies
305
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
2 days ago by
rackbersingh
• 0
0
votes
4
replies
394
views
Highest variable features in single cell data
single-cell
5 days ago by
carolofharvest
▴ 40
3
votes
4
replies
289
views
Truncated metadata file report from ENA Portal API
ena
python
2 days ago by
Giulia
• 0
2
votes
4
replies
716
views
Count all variants from vcf file
variants
vcf
Count
updated 5 days ago by
Pierre Lindenbaum
161k • written 20 months ago by
t.ali
• 0
1
vote
4
replies
391
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 2 days ago by
GenoMax
142k • written 25 days ago by
aniigodwinn
• 0
181 results • Page
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Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
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Hi ATpoint, Thanks for your reply!
Comment: How to convert normalized BigWig file to count matrix?
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• 0
Hi Pierre, Thanks for your reply! I want to get a feature count matrix from coverage data stored in BigWig files. And this BigWig file ha…
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Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
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Thank you very much, success in your projects.
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Thanks for the input :)
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This seems to indicate that the package itself (or packages it depends on) are not compatible with the R version you are using. Next step c…
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Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
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> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
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