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192 results • Page
1 of 4
Sort: Views
Rank
Views
Votes
Replies
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 4 days ago by
Ruqaiya
• 0 • written 6.4 years ago by
dllopezr
▴ 130
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
4 days ago by
vytarasov
▴ 180
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 4 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 2 days ago by
Thind amarinder
▴ 340 • written 4.9 years ago by
garbuzov
▴ 70
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 6 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 5 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 2 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 1 day ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
4
votes
3
replies
2.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 6 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
Lila M
★ 1.2k
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 3 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 1 day ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 6 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
2
votes
6
replies
1.8k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 3 hours ago by
Ram
43k • written 3.9 years ago by
millere
• 0
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
19 hours ago by
Arton
▴ 10
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 6 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 2 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
1
vote
5
replies
733
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
3
replies
690
views
Pluritest for pluripotency broken
pluripotent
pluritest
cells
stem
updated 6 days ago by
DGTool
• 0 • written 21 months ago by
yassine
• 0
2
votes
9
replies
679
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 15 hours ago by
Pierre Lindenbaum
161k • written 8 days ago by
schmince
• 0
0
votes
9
replies
572
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
2 hours ago by
Arton
▴ 10
0
votes
9
replies
571
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 9 hours ago by
Wayne
★ 2.0k • written 9 days ago by
JACKY
▴ 140
0
votes
3
replies
557
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 6 days ago by
Ram
43k • written 12 weeks ago by
maplewj
▴ 10
2
votes
5
replies
555
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 3 days ago by
arctic
▴ 40 • written 12 days ago by
M.
▴ 30
1
vote
7
replies
529
views
Question regarding WGCNA
WGCNA
Network-construction
6 days ago by
deepak
• 0
0
votes
11
replies
522
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
3 days ago by
Tuck898
• 0
0
votes
1
reply
514
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 2 days ago by
aw7
▴ 300 • written 26 days ago by
abhishekghadge
• 0
1
vote
4
replies
498
views
cellranger error message
multiplexing
cellranger
updated 5 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
3
votes
6
replies
480
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 3 days ago by
Pine
▴ 20 • written 10 days ago by
snajafy
• 0
2
votes
5
replies
479
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 1 day ago by
Ram
43k • written 7 days ago by
Prawesh
• 0
4
votes
7
replies
464
views
RNA seq analysis
DESeq
RNA-seq
15 hours ago by
Jacek
▴ 10
1
vote
1
reply
448
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 6 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
0
votes
8
replies
441
views
Different output for read length
samtools
BAM
6 days ago by
marco.barr
▴ 120
1
vote
2
replies
439
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
6 days ago by
Zeng Hao
▴ 40
3
votes
3
replies
435
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by
Jesse
▴ 770 • written 26 days ago by
yifangt86
▴ 60
1
vote
3
replies
420
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
2 days ago by
kalavattam
▴ 190
0
votes
2
replies
419
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
2 days ago by
David Langenberger
11k
0
votes
7
replies
409
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 2 days ago by
Mohamed Abderrahmane
▴ 20 • written 16 days ago by
matteo.levorato
• 0
1
vote
4
replies
404
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 5 days ago by
GenoMax
142k • written 28 days ago by
aniigodwinn
• 0
0
votes
6
replies
404
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 2 days ago by
Ram
43k • written 5 days ago by
ajbarrett98
• 0
2
votes
5
replies
398
views
Importing a fastq file
Fastq
updated 5 days ago by
size_t
▴ 120 • written 6 days ago by
oumo
• 0
4
votes
7
replies
390
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
2 days ago by
Chen
• 0
0
votes
4
replies
384
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
2 days ago by
beginner123
• 0
1
vote
9
replies
383
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 5 days ago by
i.sudbery
19k • written 8 days ago by
Assa Yeroslaviz
★ 1.8k
6
votes
7
replies
369
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
3 days ago by
sansan_96
▴ 90
1
vote
7
replies
366
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
20 hours ago by
ntsopoul
▴ 60
2
votes
6
replies
363
views
BWA alignment
Samtools
bam
updated 18 hours ago by
a.alnawfal.1992
▴ 260 • written 2 days ago by
Vahid
• 0
0
votes
1
reply
362
views
Snakemake fails to find conda in PBS
snakemake
updated 6 days ago by
tim.booth
▴ 60 • written 4 weeks ago by
yixinzeng
• 0
2
votes
8
replies
355
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Matteo Ungaro
▴ 100
1
vote
2
replies
351
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 2 days ago by
Ram
43k • written 3 days ago by
t.fortunato.asquini
• 0
192 results • Page
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Recent Votes
Answer: Using ggplotly in R
Comment: How to calculate coverage of Nanopore long read data?
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas
Answer: Cluster sub-set analysis using Seurat
Answer: Cannot install bwa-mem2 via conda
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Hi Genomax, This is the thread: https://www.biostars.org/p/9582467/ Cheers, Chris
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that's helpful, thanks :)
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These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
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