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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
255
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
6 days ago by
ramin.k2013
• 0
0
votes
0
replies
152
views
Normalization in Metagenomics Sequencing By Total Number of Reads: Pre- or Post-Filtering and the Role of Unclassified Reads
Normalization
Metagenomics
updated 7 days ago by
Ram
43k • written 8 days ago by
ramin.k2013
• 0
0
votes
1
reply
152
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
updated 8 days ago by
Pierre Lindenbaum
161k • written 8 days ago by
sainavyav22
• 0
0
votes
9
replies
546
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 7 days ago by
LauferVA
4.2k • written 8 days ago by
Aki
▴ 10
0
votes
0
replies
85
views
Issue while using circle_dat function from GOplot in R
GOplot
R
8 days ago by
ckelly96
• 0
0
votes
2
replies
173
views
Can't figure out plink --sample-diff
plink
8 days ago by
curious
▴ 750
0
votes
1
reply
135
views
Geneious Prime (Consense Sequence)
Consense
Sequence
updated 8 days ago by
GenoMax
141k • written 8 days ago by
Reno
• 0
1
vote
2
replies
203
views
convert a seurat object to expressionset
Seurat
8 days ago by
Bine
▴ 60
2
votes
4
replies
371
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 8 days ago by
GenoMax
141k • written 9 days ago by
pl.terzian
• 0
0
votes
0
replies
108
views
Inferring cell identity/genotype in single cells with missing information
cell
seurat
single
score
8 days ago by
txema.heredia
▴ 110
0
votes
0
replies
92
views
cibersortx colnames
gema122
8 days ago by
gem1
• 0
0
votes
2
replies
210
views
How to detect and visualize ORFs in bacterial genome?
statistics
visualization
ORFs
genome
6 days ago by
marongiu.luigi
▴ 710
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 9 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
0
replies
95
views
Confused about the results of a function in dada2 pipeline sample inference step
Microbiome
R
dada2
9 days ago by
Mohamed Samir
▴ 20
1
vote
4
replies
785
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
9 days ago by
Hyper_Odin
▴ 310
2
votes
4
replies
271
views
Addmetadata to seurat obj
seurat
8 days ago by
synat.keam
▴ 100
0
votes
0
replies
91
views
Methylation array analysis using dmpFinder
epic
methylation
normalization
dmp
mset
9 days ago by
Roy
▴ 10
0
votes
0
replies
180
views
Confused by the `--ld-window` flag in Vcftools. What does the number of SNPs between SNPs mean?
tabix
vcftools
9 days ago by
rijan_dhakal2055
• 0
0
votes
5
replies
372
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 8 days ago by
GenoMax
141k • written 9 days ago by
Shay
• 0
2
votes
2
replies
218
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
8 days ago by
javanokendo
▴ 60
0
votes
0
replies
96
views
Databases with GoF (Gain of Function) annotations.
gof
lof
gain-of-function
9 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
226
views
Problem with downloading genome in SnpEff
SnpEff
8 days ago by
Javier
• 0
0
votes
0
replies
95
views
Comparison between Bracken outputs
Bracken
Kraken
Taxonomy
9 days ago by
SushiRoll
▴ 120
0
votes
4
replies
256
views
Adaptive sampling for whole chromosomes
T2T
Nanopore
AdaptiveSampling
aneuploidy
centromeres
8 days ago by
njornet
▴ 20
0
votes
0
replies
112
views
DESeq2 LRT divergent DEGs ?
interaction
LRT
deseq2
9 days ago by
klervi-lugue
• 0
0
votes
2
replies
209
views
BLASTP short sequences (<20aa) - interpreting results
blast
sequence
blastp
alignment
9 days ago by
neish
• 0
0
votes
3
replies
255
views
rRNA depletion of RIP-seq samples
rRNA
RIP-seq
updated 9 days ago by
joe
▴ 500 • written 9 days ago by
CrisRisu
• 0
0
votes
1
reply
151
views
P-values for pairwise FST
FST
P-value
pairwise
updated 9 days ago by
dthorbur
★ 1.9k • written 10 days ago by
Emy
▴ 50
0
votes
4
replies
319
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 7 days ago by
GenoMax
141k • written 10 days ago by
Soohyun
• 0
0
votes
0
replies
230
views
batch correction: cds from seurat
batch-correction
R
seurat
monocle3
cds
updated 10 days ago by
Ram
43k • written 10 days ago by
sooni
▴ 20
0
votes
0
replies
136
views
Seurat Package
seurat
10 days ago by
odi
▴ 10
0
votes
0
replies
112
views
RUVg correction
differential-expression
ruvseq
updated 9 days ago by
Ram
43k • written 10 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
114
views
How to annotate pairwise p value from limma (3 groups) in a combine multiple boxplot?
limma
boxplot
9 days ago by
Chris
▴ 260
0
votes
0
replies
128
views
Methylation workflow problem
rstudio
methylation
updated 10 days ago by
Ram
43k • written 10 days ago by
Roy
▴ 10
0
votes
0
replies
121
views
ChIP-seq gene blacklist for Rattus norvegicus
rat
blacklist
ChIP-seq
10 days ago by
Thomas
• 0
2
votes
2
replies
243
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
3 days ago by
bioinfo
▴ 150
0
votes
5
replies
485
views
seg fault, core dumped with manta 1.6.0
manta
gdb
updated 10 days ago by
Ram
43k • written 14 days ago by
Greg
• 0
0
votes
1
reply
195
views
Pattern of GC content across reads from fastp
multiqc
ddRAD
updated 10 days ago by
GenoMax
141k • written 10 days ago by
jberg
• 0
2
votes
6
replies
376
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
10 days ago by
jkim
▴ 170
0
votes
0
replies
108
views
RNA velocity after SoupX in single cell data
soupX
scrna
transcriptomics
nuclei
updated 10 days ago by
GenoMax
141k • written 10 days ago by
shersky
• 0
0
votes
0
replies
103
views
What is more important for Structural Variant Calling? Recall or Precision?
structural-variants
merging
precision-recall
10 days ago by
Luke
• 0
1
vote
1
reply
446
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 10 days ago by
chrchang523
10k • written 10 days ago by
dsbusiness135
▴ 10
1
vote
2
replies
190
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
10 days ago by
phhelou5
• 0
0
votes
1
reply
257
views
How to do further funtional analysis of DEG KeggGet output list?
KEGGREST
DESEQ2
RNA-Seq
DEG
10 days ago by
joana.maclean
• 0
8
votes
10
replies
658
views
bash script
whole-genome-sequencing
updated 3 days ago by
Ram
43k • written 10 days ago by
bestone
▴ 30
0
votes
0
replies
111
views
Confusion with somatic variant calling: Advice on Ensembl-compatible resources?
GATK
Mutect2
ensembl
9 days ago by
DGTool
• 0
1
vote
1
reply
158
views
permutation test in edgeR
rna-seq
edgeR
updated 10 days ago by
dariober
14k • written 11 days ago by
Netanel
• 0
0
votes
0
replies
263
views
Different rsID for the same chromsome, position, ref & alt allele depending on different data sources. Which one should I use?
UKB
rsID
UKB-PPP
ensembl-vep
dbsnp
8 days ago by
lsy9
▴ 20
0
votes
0
replies
122
views
How can I plot the PCA with the raw count mRNA seq data?
PCA
normalization
updated 10 days ago by
Ram
43k • written 11 days ago by
Yoomi
▴ 20
0
votes
0
replies
111
views
Blast2GO Fisher test
Fisher-test
Go-annotation
Blast2GO
updated 10 days ago by
Ram
43k • written 11 days ago by
BlackM
• 0
1,000 results • Page
3 of 20
Recent Votes
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
How to compare the quality of assemblies
Filtration Of Reads With Length Lower Than 30 From Bam
Answer: Filtration Of Reads With Length Lower Than 30 From Bam
Answer: How to compare the quality of assemblies
Comment: How to compare the quality of assemblies
Bedtools merge but only if intersection exists
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Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't amongst your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry a…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
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Pierre Lindenbaum
161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
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b.contreras.moreira
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My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
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6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
Comment: Korean human genome reference file
by
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Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
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thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
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by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
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▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
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