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485 results • Page
4 of 10
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0
votes
2
replies
262
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 12 days ago by
Ram
43k • written 12 days ago by
David
• 0
0
votes
2
replies
268
views
RNAseq 1 control 2 different treatment
RNA-seq
12 days ago by
matteo.levorato
• 0
0
votes
2
replies
202
views
Can't figure out plink --sample-diff
plink
18 days ago by
curious
▴ 750
0
votes
2
replies
579
views
Bacterial contamination in human DNA sample
Long-read-sequencing
Bacterial-contamination
updated 23 days ago by
Ram
43k • written 22 months ago by
priya.bmg
▴ 60
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 10 days ago by
Ram
43k • written 6.6 years ago by
Alternative
▴ 270
0
votes
2
replies
251
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 4 days ago by
Ram
43k • written 4 days ago by
v.berriosfarias
▴ 140
1
vote
2
replies
1.0k
views
An issue with application of SPAdes genome assembly in Galaxy
Galaxy
SPAdes
updated 26 days ago by
Ram
43k • written 2.4 years ago by
adnan.lahuf
• 0
2
votes
2
replies
631
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 11 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
1
vote
2
replies
226
views
convert a seurat object to expressionset
Seurat
17 days ago by
Bine
▴ 60
0
votes
2
replies
228
views
HWE filter of vcf files
snp
vcf.
26 days ago by
Max
• 0
1
vote
2
replies
209
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
20 days ago by
phhelou5
• 0
0
votes
2
replies
229
views
Bedmethyl file format
bedmethyl
methylation
updated 11 days ago by
GenoMax
141k • written 11 days ago by
njornet
▴ 20
2
votes
2
replies
276
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 17 days ago by
ATpoint
82k • written 17 days ago by
Shicheng Guo
★ 9.4k
0
votes
2
replies
223
views
BLASTP short sequences (<20aa) - interpreting results
blast
sequence
blastp
alignment
18 days ago by
neish
• 0
1
vote
2
replies
321
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 13 days ago by
Istvan Albert
100k • written 14 days ago by
Jiang
• 0
0
votes
2
replies
322
views
GSEA analysis in R
GSEA
R
Arabidopsis
10 days ago by
Sudip
• 0
2
votes
2
replies
266
views
Removing adapters in all the RNAseq samples regardless if they have or not, is it correct?
fastqc
trimming
adapters
cutadapt
RNAseq
updated 24 days ago by
dsull
★ 5.9k • written 25 days ago by
ev97
▴ 20
1
vote
2
replies
240
views
permutation test in edgeR
rna-seq
edgeR
updated 6 days ago by
Gordon Smyth
★ 7.0k • written 20 days ago by
Netanel
• 0
1
vote
2
replies
636
views
Nanopore multisample variant calling
SNPs
nanopore
SNP-calling
variants
multisample
29 days ago by
colindaven
6.4k
0
votes
2
replies
375
views
I can't add VAF from population for all of my variants from VCF file
vaf
vcf
genomics
gnomad
allelicfrequency
28 days ago by
Samuel
▴ 20
0
votes
2
replies
274
views
How to get genes in a gene set in msigdb?
msigdb
23 days ago by
Chris
▴ 260
0
votes
2
replies
542
views
autodockvina
python
python3
autodock
updated 9 days ago by
Ram
43k • written 4 months ago by
iamsmor
• 0
0
votes
2
replies
220
views
RNA-Seq isoforms identification
RNA-seq
updated 25 days ago by
Andres
▴ 20 • written 25 days ago by
latita.atun
• 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 11 days ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
1
vote
2
replies
273
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
11 days ago by
bioinfo
▴ 150
1
vote
2
replies
811
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 11 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
0
votes
2
replies
272
views
bam merging for archaic samples
samtools
bam
updated 7 days ago by
Ram
43k • written 8 days ago by
Matteo Ungaro
▴ 100
4
votes
2
replies
234
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa
samtools
mapping
genome
updated 24 days ago by
Pierre Lindenbaum
161k • written 24 days ago by
Lee
• 0
0
votes
2
replies
270
views
Regions not clear in VCF
whole-exome
variant-calling
updated 20 days ago by
Ram
43k • written 21 days ago by
priya.bmg
▴ 60
0
votes
2
replies
513
views
Gene expression assay Yeast sample prep
Live-cells
updated 26 days ago by
Ram
43k • written 22 months ago by
dshdixit
▴ 10
1
vote
2
replies
279
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 11 days ago by
Ram
43k • written 11 days ago by
aniigodwinn
• 0
1
vote
2
replies
927
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 23 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
0
votes
2
replies
255
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
11 days ago by
DKA
▴ 40
0
votes
2
replies
625
views
Seeking Alternative Tools for Predicting Mature microRNAs from Vertebrate Animal Precursors in In Silico Study
mirdeep2
maturebayes
microrna
updated 26 days ago by
Ram
43k • written 12 months ago by
Beatriz
• 0
0
votes
2
replies
252
views
Problem with downloading genome in SnpEff
SnpEff
18 days ago by
Javier
• 0
0
votes
2
replies
255
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
11 days ago by
mropri
▴ 150
0
votes
2
replies
322
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
15 days ago by
O.rka
▴ 710
0
votes
1
reply
299
views
Sheep-Human ortholog mapping with BioMart and Orthogene/Gprofiler
ortholog
sheep
updated 20 days ago by
Shuang He
• 0 • written 3 months ago by
Michael
• 0
0
votes
1
reply
186
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA
substitution
VCFstats
Evolution
VCF
updated 17 days ago by
Pierre Lindenbaum
161k • written 17 days ago by
Saran
▴ 50
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects
RNA-Seq
batch-effect
updated 11 days ago by
Ram
43k • written 6.8 years ago by
Dipro
• 0
0
votes
1
reply
233
views
Design matrix after RUVg correction
limma
ruvseq
differential-expression
updated 19 days ago by
Ram
43k • written 11 weeks ago by
Shaimaa Gamal
▴ 10
0
votes
1
reply
77
views
Downloading full alignments from Pfam
pfam
updated 4 hours ago by
GenoMax
141k • written 8 hours ago by
bef1
• 0
0
votes
1
reply
245
views
eQTL analysis of GWAS summary statistics, missing GT values
Genomics
eQTL
GWAS
updated 23 days ago by
Ram
43k • written 12 weeks ago by
Orlando
• 0
1
vote
1
reply
409
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
9 days ago by
renan.igor
• 0
0
votes
1
reply
234
views
Need help with improving the 16S rRNA sequence quality with trimmomatic?
bioinformatic
Trimmomatic
updated 26 days ago by
gv
• 0 • written 29 days ago by
Kai Xin
• 0
0
votes
1
reply
210
views
POD5 files
ONT
updated 23 days ago by
GenoMax
141k • written 23 days ago by
marco.barr
▴ 80
2
votes
1
reply
169
views
multiple reference sequences
freebayes
updated 26 days ago by
GenoMax
141k • written 26 days ago by
emilydolivo97
▴ 10
0
votes
1
reply
229
views
AUC=1, is it possible after lasso regression?
lasso
AUC
updated 27 days ago by
Jeremy Leipzig
22k • written 29 days ago by
Amir
• 0
0
votes
1
reply
251
views
Bowtie2 alignment rate
galaxy
Bowtie
alignment-rate
updated 26 days ago by
gv
• 0 • written 4 weeks ago by
pavithraashokkumar818
• 0
1
vote
1
reply
414
views
Long reads Annotation
long-reads
pacbio
updated 23 days ago by
Ram
43k • written 2.1 years ago by
Gerardo
• 0
485 results • Page
4 of 10
Recent Votes
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Batch effects : ComBat or removebatcheffects (limma package) ?
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Recent Replies
Comment: What does it mean single base resolution in sequencing?
by
dsull
★ 5.9k
Great comprehensive explanation and overview of the technologies -- with regards to sequencing assays, the one thing I'd add is SNV identif…
Answer: What does it mean single base resolution in sequencing?
by
dsull
★ 5.9k
I think that term means slightly different things in different contexts. For example, it's useful to profile mRNA modifications (e.g. m6a) …
Answer: Cannot process all the reads in a fast5 file?
by
chujie
• 0
Hi, I met the same problem, have you found the solution?
Answer: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
Hi @fe3e6f65 , In a single sentence, the answer to your question can be summarized as, "*the resolution of a genomic technology refers to …
Comment: PCA plot
by
LauferVA
4.2k
Without more context, we cannot interpret this PCA plot. There are many possibilities. In addition, this question is basic enough that it w…
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by
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22k
i have the name ready: out**liar**
Comment: What does it mean single base resolution in sequencing?
by
GenoMax
141k
Sequencing by hybridization (https://en.wikipedia.org/wiki/Sequencing_by_hybridization ) is likely not giving you single base resolution. B…
Comment: Fetch table from clinvar database according to a list of rsid
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▴ 20
Hii... i have updated the script in python..But, still getting no data found. Actually the data is there, i have print the parsed html file…
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ATpoint
82k
https://bioconductor.org/books/release/OSCA.multisample/using-corrected-values.html
Comment: Downloading full alignments from Pfam
by
GenoMax
141k
Not as convenient but the entire set of full alignments can be downloaded here: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pf…
Comment: How many reads for WGS Sequencing?
by
GenoMax
141k
> What does clipped Fastq mean? Probably means that NCBI has already scanned and trimmed adapter sequencers. > both forward and revers…
Comment: How many reads for WGS Sequencing?
by
GenoMax
141k
You can use the default `adapters.fa` file included in the `resources` folder of [**BBMap suite**][1] (program to use is `bbduk.sh`) or a p…
Comment: How many reads for WGS Sequencing?
by
GenoMax
141k
Only way to find out is to try. It may work but if it is not going to then you will find that out quick (process would likely crash because…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Also, there is no mention of adapter sequence so which adapter sequence should i use to remove it from some other reads?
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Also, Do you think i can reproduce at least most part of the data from the paper just on my laptop? It has 4 logical processors (Intel(R) C…
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