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36 results • Page
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12
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Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
features
Marker
ArchR
34 minutes ago by
naomiboldon
• 0
0
votes
3
replies
45
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
converter
liftover
updated 39 minutes ago by
Giulio Genovese
▴ 390 • written 1 hour ago by
Omics data mining
▴ 260
1
vote
7
replies
434
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 3 hours ago by
Pierre Lindenbaum
161k • written 2 days ago by
schmince
• 0
0
votes
4
replies
96
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
updated 1 hour ago by
GenoMax
142k • written 4 hours ago by
SilhouetteQ
• 0
0
votes
1
reply
41
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 3 hours ago by
GenoMax
142k • written 3 hours ago by
maria.soler
• 0
0
votes
0
replies
37
views
How are score_weights calculated in this code?
cell
single
4 hours ago by
carolofharvest
▴ 40
0
votes
0
replies
44
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
6 hours ago by
SeoGyun
• 0
0
votes
0
replies
47
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
8 hours ago by
Samantha
• 0
0
votes
1
reply
78
views
Microbial Signal Transduction Database
MiST
updated 6 hours ago by
zx8754
11k • written 9 hours ago by
Shravani
• 0
0
votes
0
replies
44
views
input file in rmats
rmats
updated 6 hours ago by
zx8754
11k • written 8 hours ago by
Lambodarswain316
• 0
0
votes
1
reply
90
views
DESeq2 error
DESeq2
updated 9 hours ago by
ATpoint
82k • written 12 hours ago by
sooni
▴ 20
0
votes
0
replies
44
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
10 hours ago by
singcell
• 0
0
votes
1
reply
101
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 7 hours ago by
ATpoint
82k • written 10 hours ago by
Amr
▴ 160
0
votes
2
replies
97
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
8 hours ago by
jain72744
▴ 10
0
votes
0
replies
45
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
10 hours ago by
jain72744
▴ 10
5
votes
2
replies
103
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 10 hours ago by
Gordon Smyth
★ 7.1k • written 12 hours ago by
gBioStar5
▴ 10
2
votes
5
replies
262
views
Importing a fastq file
Fastq
updated 12 hours ago by
size_t
▴ 120 • written 1 day ago by
oumo
• 0
3
votes
1
reply
79
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 3 hours ago by
dthorbur
★ 1.9k • written 15 hours ago by
Eren
• 0
0
votes
0
replies
58
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
16 hours ago by
Aytaç
• 0
0
votes
0
replies
66
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 6 hours ago by
zx8754
11k • written 17 hours ago by
curious_butterfly
• 0
0
votes
0
replies
63
views
supervised admixture
supervised
admixture
18 hours ago by
RT
▴ 10
0
votes
0
replies
67
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization
Mendelian
two-sample
20 hours ago by
Nikki
• 0
2
votes
0
replies
67
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
20 hours ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
308
views
Different output for read length
samtools
BAM
19 hours ago by
marco.barr
▴ 100
0
votes
1
reply
282
views
Snakemake fails to find conda in PBS
snakemake
updated 22 hours ago by
tim.booth
▴ 60 • written 28 days ago by
yixinzeng
• 0
0
votes
2
replies
137
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 22 hours ago by
GenoMax
142k • written 23 hours ago by
sainavyav22
• 0
2
votes
3
replies
158
views
Truncated metadata file report from ENA Portal API
ena
python
updated 4 hours ago by
GenoMax
142k • written 23 hours ago by
Giulia
• 0
0
votes
3
replies
222
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
updated 13 hours ago by
Philipp Bayer
8.4k • written 1 day ago by
rackbersingh
• 0
1
vote
3
replies
211
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 23 hours ago by
GenoMax
142k • written 1 day ago by
cput
• 0
3
votes
5
replies
313
views
RNA seq analysis
DESeq
RNA-seq
3 hours ago by
prifa
▴ 10
1
vote
9
replies
308
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 2 hours ago by
i.sudbery
19k • written 3 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
3
replies
198
views
Correlation Analysis
statistics
methylation
NGS
expression
updated 5 hours ago by
manaswwm
▴ 510 • written 3 days ago by
Researcher
▴ 30
1
vote
3
replies
296
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 20 hours ago by
bk11
★ 2.4k • written 5 days ago by
Yoosef
▴ 60
3
votes
3
replies
416
views
absolute path for symbolic links in Snakefile
Snakemake
updated 17 hours ago by
Jesse
▴ 770 • written 20 days ago by
yifangt86
▴ 60
1
vote
4
replies
447
views
cellranger error message
multiplexing
cellranger
updated 39 minutes ago by
Max
• 0 • written 12 weeks ago by
Alivia
▴ 10
36 results • Page
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Comment: Question about methylation location
Comment: Question about methylation location
Comment: Question about methylation location
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
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maria.soler
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Comment: cellranger error message
by
Max
• 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Giulio Genovese
▴ 390
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Pierre Lindenbaum
161k
I think this is useless, in the gatk doc: > For each variant, the tool will look for the target coordinate, reverse-complement and left-al…
Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
142k
Ideally you will know which adapters to use but if you don't then programs like `fastp` can auto-detect them. You could also use `bbduk.sh`…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
With the `--read2-only` option (which isn't available yet on the bioconda version), this will complain about a lack of `--bc-pattern`. How…
Comment: samtools tview symbols
by
Ruqaiya
• 0
What does the star mean then ?
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…
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