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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
3
replies
41
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
15 minutes ago by
SilhouetteQ
• 0
0
votes
1
reply
21
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 50 minutes ago by
GenoMax
142k • written 52 minutes ago by
maria.soler
• 0
0
votes
0
replies
21
views
How are score_weights calculated in this code?
cell
single
1 hour ago by
carolofharvest
▴ 40
0
votes
0
replies
30
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
3 hours ago by
SeoGyun
• 0
0
votes
0
replies
38
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
5 hours ago by
Samantha
• 0
0
votes
1
reply
65
views
Microbial Signal Transduction Database
MiST
updated 3 hours ago by
zx8754
11k • written 6 hours ago by
Shravani
• 0
0
votes
0
replies
33
views
input file in rmats
rmats
updated 3 hours ago by
zx8754
11k • written 5 hours ago by
Lambodarswain316
• 0
0
votes
0
replies
34
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
7 hours ago by
singcell
• 0
0
votes
1
reply
86
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 4 hours ago by
ATpoint
82k • written 7 hours ago by
Amr
▴ 160
0
votes
2
replies
83
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
5 hours ago by
jain72744
▴ 10
0
votes
0
replies
36
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
7 hours ago by
jain72744
▴ 10
0
votes
1
reply
57
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 30 minutes ago by
dthorbur
★ 1.9k • written 12 hours ago by
Eren
• 0
0
votes
0
replies
52
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
13 hours ago by
Aytaç
• 0
0
votes
0
replies
61
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 3 hours ago by
zx8754
11k • written 14 hours ago by
curious_butterfly
• 0
0
votes
0
replies
57
views
supervised admixture
supervised
admixture
15 hours ago by
RT
▴ 10
0
votes
0
replies
62
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization
Mendelian
two-sample
17 hours ago by
Nikki
• 0
0
votes
2
replies
132
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 19 hours ago by
GenoMax
142k • written 20 hours ago by
sainavyav22
• 0
2
votes
3
replies
126
views
Truncated metadata file report from ENA Portal API
ena
python
updated 1 hour ago by
GenoMax
142k • written 20 hours ago by
Giulia
• 0
0
votes
0
replies
67
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
21 hours ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
95
views
input file for alternative splicing in rmats in linux
rmats
updated 21 hours ago by
Ram
43k • written 1 day ago by
Lambodarswain316
• 0
1
vote
1
reply
401
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 1 day ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
1
vote
0
replies
96
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
1 day ago by
Shae
▴ 10
1
vote
1
reply
118
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 1 day ago by
andres.firrincieli
3.6k • written 1 day ago by
kacollier
▴ 30
0
votes
0
replies
94
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
98
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
1 day ago by
Zeng Hao
▴ 40
1
vote
3
replies
204
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 20 hours ago by
GenoMax
142k • written 1 day ago by
cput
• 0
0
votes
0
replies
104
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
1 day ago by
asalimih
▴ 60
0
votes
2
replies
223
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 1 day 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
0
replies
95
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
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 1 day ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
3
votes
5
replies
286
views
RNA seq analysis
DESeq
RNA-seq
10 minutes ago by
prifa
▴ 10
0
votes
0
replies
136
views
Chance for trained without experience
bio
updated 2 days ago by
ATpoint
82k • written 2 days ago by
shehab
• 0
0
votes
0
replies
113
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
2 days ago by
Omics data mining
▴ 260
0
votes
2
replies
161
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
2 days ago by
njornet
▴ 20
0
votes
2
replies
187
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
Darya
• 0
0
votes
5
replies
223
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 2 days ago by
Joe
21k • written 2 days ago by
Lemonhope
• 0
0
votes
0
replies
155
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
1 day ago by
Winter
• 0
0
votes
0
replies
84
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
2 days ago by
analyst
▴ 50
0
votes
0
replies
98
views
meffil.snp.concordance
meffil
methylation
snp_concordance
2 days ago by
kyj222637
• 0
0
votes
1
reply
139
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 1 day ago by
Bastien Hervé
5.3k • written 2 days ago by
sooni
▴ 20
0
votes
3
replies
217
views
STAR aligner error
RNA-seq
STAR
slurm
updated 1 day ago by
Ram
43k • written 2 days ago by
M.
▴ 30
0
votes
0
replies
93
views
monocle 3-- Could not get node in small cluster
monocle3
2 days ago by
synat.keam
▴ 100
0
votes
2
replies
190
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
1 day ago by
Nicholas
• 0
0
votes
1
reply
211
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Sony
▴ 10
5
votes
5
replies
265
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
2 days ago by
Chris
▴ 280
0
votes
2
replies
201
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 1 day ago by
swbarnes2
14k • written 3 days ago by
ahmad.sajad4541
• 0
1
vote
8
replies
264
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
1 hour ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
156
views
student
epitranscriptomics
updated 3 days ago by
ATpoint
82k • written 3 days ago by
useriwa
• 0
0
votes
0
replies
107
views
Imputation of missing genotypes
panel
beagle
imputation
3 days ago by
analyst
▴ 50
1,000 results • Page
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Recent Votes
How to use minimap2?
Comment: RNA seq analysis
Comment: Filtering Multi-sample VCF file for all except one Genotype
Truncated metadata file report from ENA Portal API
Comment: Truncated metadata file report from ENA Portal API
A: Download data from TCGA
A: Do I need to normalize level 3 TCGA data?
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Popular Question
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maria.soler
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Popular Question
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melissachua90
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Lila M
★ 1.2k
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Recent Replies
Comment: RNA seq analysis
by
prifa
▴ 10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
Answer: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> The goal is to remove all the variants which are unique to the KWSBambina sample. using jvarkit vcffilterjdk https://jvarkit.readthedo…
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
The first example used the adapter file NexteraPE-PE.fa, but it generated more than 50% unpaired data...... The content of NexteraPE-PE.fa…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
Ok so I definitely didn't understand at first what my goal was. The goal is to remove all the variants which are unique to the KWSBambina…
Comment: Question about methylation location
by
dthorbur
★ 1.9k
What data do you have? Generally, you start with sequencing data, which you need to clean and then map to a reference genome. Then dependin…
Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
142k
> when I didn't provide the adapter file Still see the file here `ILLUMINACLIP:./NexteraPE-PE.fa:2:30:10 `, unless that is an empty file.
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
Interestingly, when I didn't provide the adapter file, the number of unpaired forward reads was significantly reduced: TrimmomaticPE…
Comment: Alignment of samples with spike-in
by
GenoMax
142k
> but then if you only allow to map uniquely mapped reads, you are losing spike-in information, How so? Spike-in's are generally unique s…
Comment: Truncated metadata file report from ENA Portal API
by
GenoMax
142k
While there is no timeout by default on the `get` operation, you may want to set a higher value and see if that helps, since there is a lar…
Comment: Truncated metadata file report from ENA Portal API
by
Giulia
• 0
The " missing is because of a copy-paste error in the post.. I know wget but my tool is entirely in python. I really don't understand why i…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
and if I use the command as such: ``` umi_tools extract --extract-method=regex --error-correct-cell \ --bc-pattern2='(?P…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
No, UMI-tools won't work this out automatically, you'll need to either switch read1 and read2 or use the new `--read2-only` which is curren…
Comment: Correlation Analysis
by
manaswwm
▴ 510
If your *gene_corr* data frame contains one gene instead of all genes, then the correlation would be per gene. If your *gene_corr* data fra…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
I think I might know my problem. The barcodes are in this case on read2 and not on read1. Does umi-tools recognise it automatically, or do …
Comment: Microbial Signal Transduction Database
by
zx8754
11k
Did you try https://mib-jouline-db.asc.ohio-state.edu/#introduction ? >The database can also be accessed via the API. The same API points …
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