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185 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 3 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
3 days ago by
vytarasov
▴ 180
9
votes
7
replies
7.1k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 3 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 23 hours 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 4 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 3 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 6 days ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.5k
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 14 hours ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 5 days ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 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 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
Lila M
★ 1.2k
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 2 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 2 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS
insertion site
trangene
de-novo
soap
updated 5 days ago by
Cameron.walker9900
• 0 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 2 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
0
votes
4
replies
2.2k
views
MGLTools does not work in windows 11
Autodock
MGLTools
windows
windows11
updated 10 hours ago by
Ashfaq
• 0 • 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 5 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 5 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 5 days ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 13 hours ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 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 6 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
13
votes
14
replies
877
views
High Malat-1 expression in single cell data
single-cell
updated 6 days ago by
t.montserrat.ayuso
▴ 40 • written 15 days ago by
carolofharvest
▴ 40
0
votes
3
replies
685
views
Pluritest for pluripotency broken
pluripotent
pluritest
cells
stem
updated 5 days ago by
DGTool
• 0 • written 21 months ago by
yassine
• 0
1
vote
7
replies
589
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 4 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
schmince
• 0
0
votes
3
replies
548
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 4 days ago by
Ram
43k • written 11 weeks ago by
maplewj
▴ 10
2
votes
5
replies
533
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 1 day ago by
arctic
▴ 40 • written 10 days ago by
M.
▴ 30
1
vote
7
replies
511
views
Question regarding WGCNA
WGCNA
Network-construction
4 days ago by
deepak
• 0
0
votes
7
replies
495
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 5 days ago by
Wayne
★ 2.0k • written 7 days ago by
JACKY
▴ 140
1
vote
4
replies
488
views
cellranger error message
multiplexing
cellranger
updated 3 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
0
votes
11
replies
487
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
1 day ago by
Tuck898
• 0
0
votes
2
replies
474
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 6 days ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
3
votes
6
replies
471
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 1 day ago by
Pine
▴ 20 • written 8 days ago by
snajafy
• 0
1
vote
1
reply
442
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 5 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
0
votes
1
reply
432
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 1 day ago by
aw7
▴ 280 • written 24 days ago by
abhishekghadge
• 0
1
vote
2
replies
432
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
5 days ago by
Zeng Hao
▴ 40
1
vote
5
replies
429
views
HCL database download
HCL
updated 6 days ago by
Ram
43k • written 10 days ago by
sooni
▴ 20
3
votes
3
replies
428
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by
Jesse
▴ 770 • written 24 days ago by
yifangt86
▴ 60
0
votes
8
replies
425
views
Different output for read length
samtools
BAM
4 days ago by
marco.barr
▴ 110
4
votes
6
replies
400
views
RNA seq analysis
DESeq
RNA-seq
updated 1 day ago by
Matthias Zepper
4.6k • written 6 days ago by
prifa
▴ 10
1
vote
4
replies
400
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 3 days ago by
GenoMax
142k • written 26 days ago by
aniigodwinn
• 0
0
votes
7
replies
399
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 1 day ago by
Mohamed Abderrahmane
▴ 20 • written 15 days ago by
matteo.levorato
• 0
2
votes
5
replies
386
views
Importing a fastq file
Fastq
updated 4 days ago by
size_t
▴ 120 • written 5 days ago by
oumo
• 0
0
votes
2
replies
382
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
17 hours ago by
David Langenberger
11k
4
votes
7
replies
378
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
13 hours ago by
Chen
• 0
0
votes
6
replies
377
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 15 hours ago by
Ram
43k • written 3 days ago by
ajbarrett98
• 0
1
vote
4
replies
376
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
6 days ago by
heelpPlease
• 0
1
vote
4
replies
362
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 17 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
9
replies
361
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 4 days ago by
i.sudbery
19k • written 7 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
359
views
Snakemake fails to find conda in PBS
snakemake
updated 4 days ago by
tim.booth
▴ 60 • written 4 weeks ago by
yixinzeng
• 0
0
votes
4
replies
357
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
1 day ago by
beginner123
• 0
1
vote
5
replies
348
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 6 days ago by
Michael
54k • written 7 days ago by
qwertyuiop26
• 0
185 results • Page
1 of 4
Recent Votes
A: GC bias correction for Chip-SEQ
Comment: Help with IGV abbreviation
A: How to get read counts on transcript level using featurecounts?
Answer: Vcf file sorting
Answer: How to interpret infinite odds ratio?
Answer: Is there any way to modify this pie chart ?
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
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Recent Replies
Comment: How to access GWAVA software of data
by
GenoMax
142k
Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
Comment: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Answer: Overlapping Ranges within Granges object
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82k
There is no one-hit function in GenomicRanges, but you can stick something together using a combination of `findOverlaps` to first find ove…
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• 0
Hi, I did not encounter any " \ - " characters in the fastq input files, and it doesn't seem to be present in any other files either. Thank…
Comment: How to interpret infinite odds ratio?
by
Lukas
• 0
Thanks you for your answer. But according that links interpretation of inf odds ratio is up to hypothesis of the researcher.So my solution …
Comment: How to access GWAVA software of data
by
nonaddldy
▴ 10
Not found in https://ftp.sanger.ac.uk/resources/software/gwava/ ![][1] [1]: /media/images/f69695ec-e047-44f6-95ce-cd4edf1c
Comment: How to access GWAVA software of data
by
nonaddldy
▴ 10
https://www.sanger.ac.uk/tool/gwava/
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK
by
IdaHao0921
• 0
The species I study is not a model species, VQSR can not be applied here. I already used gatk hard-filtering. I mean, after hard-filtering,…
Answer: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
If you're not tied to Granges, you could use `bedmap --fraction-both 0.1` to require at least 10% overlap between reference and map regions…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
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▴ 30
By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process…
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by
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▴ 30
I have tried installing AGAT. But it failed the tests. …
Comment: BWA alignment
by
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82k
That is not what the logs above tell, but good you solved it.
Answer: Inquiry about deseq2 transformation
by
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82k
The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
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