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899 results • Page
2 of 18
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
100
views
Biomark Fluidigm delta delta CT method calculation
Fluidigm
Biomark
qPCR
4 days ago by
jms2520
▴ 20
0
votes
0
replies
92
views
pyscenic cannot mapped to the feather file
pyscenic
4 days ago by
Andy
▴ 30
0
votes
0
replies
84
views
How to calculate Summary.csv statistics after re-running STARSolo cell filtering?
scRNA-seq
STARSolo
STAR
4 days ago by
ayeTown
• 0
0
votes
0
replies
96
views
Solving set of equations possibly with Matlab for affinity measurement with ELISA
set
ELISA
affinity
Matlab
equation
4 days ago by
field654
▴ 30
0
votes
0
replies
97
views
how to get the nucleotide squence behind a symbolic ALT in VCF
SV
vcf
sniffles
2 days ago by
Maxine
• 0
0
votes
0
replies
154
views
How can I retrive the actual amino acid and the alternative amino acid (if any cordon changes happened due to editing)?
RNA
editing
4 days ago by
Genetics
▴ 20
0
votes
0
replies
89
views
pyscenic feather file
pyscenic
4 days ago by
Andy
▴ 30
1
vote
1
reply
148
views
Is there a site that takes a list of uniprot IDs/gene IDs as input and create radial phylogenetic tree?
phylogenetictree
4 days ago by
Diwan
▴ 650
0
votes
0
replies
85
views
Something wrong with my code concerning bsseq visualization
bsseq
plotRegion
R
4 days ago by
diqixiaoyaoer
▴ 10
0
votes
0
replies
93
views
How to bifurcate patients into high and low expressing groups for TCGA survival analysis for a gene of interest
Meidan
TCGA
Percentile
Survival
R
4 days ago by
Manav
• 0
1
vote
3
replies
199
views
TSV with multi-allelic sites to VCF
bcftools
updated 4 days ago by
barslmn
★ 1.3k • written 4 days ago by
Christian
▴ 20
0
votes
0
replies
112
views
Spearman correlation rna-seq gene to blood values
spearman
rna-seq
3 days ago by
bas2020
▴ 20
4
votes
3
replies
189
views
Geom bar postive and negative values in a flipped plot
flip_coord
ggplot
geom_bar
3 days ago by
luzglongoria
▴ 40
3
votes
8
replies
290
views
getting coding exon information from Ensembl API
Ensembl
API
updated 4 days ago by
Ram
38k • written 4 days ago by
Nobody
▴ 30
0
votes
0
replies
101
views
displaying results of different RNA-seq projects in R shiny
RNA-seq
shiny
R
4 days ago by
rls_08
▴ 40
2
votes
3
replies
210
views
RNAseq: same reads + more complete scaffold = fewer DEGs?
RNAseq
updated 3 days ago by
Darked89
4.2k • written 4 days ago by
phillip.brassington
▴ 10
0
votes
0
replies
94
views
calc IBS with vcf files with different snfs
IBS
PLINK
3 days ago by
Mali
• 0
0
votes
0
replies
89
views
Hi-C aggregation plot | ARA | PE-Scan
Hi-C
4 days ago by
Argonaut
• 0
1
vote
3
replies
159
views
Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?
QC
cutadapt
Illumina
trimming
3.4
updated 4 days ago by
GenoMax
127k • written 4 days ago by
Bengisu
• 0
1
vote
3
replies
189
views
What is exactly meant by "GENCODE TSS"?
GENCODE
transcription
annotation
TSS
gene
4 days ago by
ConvolutedGenome
▴ 10
0
votes
3
replies
220
views
SRA Taxonomy Analysis - difference between tables and web
athena
taxonomy
sra
cloud
updated 3 days ago by
GenoMax
127k • written 5 days ago by
Art_SG
• 0
0
votes
0
replies
97
views
inquiry related to Hi-C data download
Hi-C
datasets
human
brain-cortex
interaction
matrix
5 days ago by
rheab1230
▴ 140
3
votes
4
replies
262
views
Creating sample groups from a combination of genes for survival analysis
Survival
4 days ago by
krushnach80
★ 1.1k
3
votes
2
replies
160
views
Power analysis for patient samples
RNA-seq
5 days ago by
aropri
▴ 130
0
votes
2
replies
154
views
OrthoFinder problem
Sub
OrthoFinder
iterative
processes
Bash
4 days ago by
HERMAN
▴ 10
0
votes
1
reply
133
views
Error when using compareCluster from enichment
compareCluster
updated 5 days ago by
Basti
★ 1.4k • written 5 days ago by
jacob
• 0
0
votes
0
replies
97
views
Need Help Scraping MeSH terms from Pubmed
Python
Entrez
Scraping
updated 5 days ago by
Ram
38k • written 5 days ago by
Arnau
• 0
1
vote
1
reply
120
views
NA14622 data for benchmarking
benchmarking
vcf
bed
GiAB
updated 5 days ago by
GenoMax
127k • written 5 days ago by
emmanouil.a
▴ 110
0
votes
2
replies
169
views
How to add gene information below the BSmooth result ?
BSmooth
methylation
DNA
5 days ago by
diqixiaoyaoer
▴ 10
1
vote
1
reply
153
views
Plot in R: Presence of bacteria type A vs bacteria type B in different groups
boxplot
phyloseq
plot
abundance
ggplot2
R
updated 5 days ago by
Basti
★ 1.4k • written 5 days ago by
flourde
• 0
1
vote
5
replies
324
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
updated 5 days ago by
Trivas
▴ 710 • written 5 days ago by
TJay
• 0
1
vote
1
reply
144
views
Why GATK is slow with haplotypecalling
GATK
HaplotypeCalling
updated 5 days ago by
Pierre Lindenbaum
153k • written 5 days ago by
rj.rezwan
• 0
0
votes
0
replies
102
views
How to shift the position of multiallelic variants for phasing analysis with SHAPEIT2?
NGS
bcftools
vcf
phase
5 days ago by
zhangfish
▴ 40
0
votes
0
replies
88
views
Homer annotatePeaks for enrichment analysis
annotatePeaks
homer
DMR
methylation
5 days ago by
Joana
• 0
0
votes
0
replies
124
views
Seurat analysis without ribosomal genes
single-cell
transcriptomics
seurat
5 days ago by
firestar
★ 1.5k
0
votes
0
replies
114
views
Add HI:i:<n> tag to a BAM file
SAM
hisat2
STAR
tag
BAM
5 days ago by
predeus
★ 1.8k
0
votes
0
replies
114
views
Quality control of the X-chromosome for use in a GWAS using REGENIE
REGENIE
GWAS
LMM
chromosome-X
quality-control
5 days ago by
ucbtep
▴ 20
0
votes
0
replies
138
views
Dnaplotter
Artemis
6 days ago by
prs
• 0
2
votes
1
reply
211
views
How to create GO Bar Plot using data obtained from DAVID Functional Enrichment Analysis?
Plot
DAVID
R
updated 5 days ago by
Basti
★ 1.4k • written 6 days ago by
Stefanus C.B.
• 0
0
votes
2
replies
217
views
mrbayes segmentation fault
mrbayes
segmentation
fault
4 days ago by
dgrace999
• 0
0
votes
0
replies
130
views
Obtain the GenomicRanges from segmented CNA data and the corresponding TSS for EnrichedPlot
TSS
GRanges
EnrichedPlot
promoters
GenomicRanges
6 days ago by
melissachuaphd
• 0
0
votes
0
replies
121
views
ChIPseq w/ polyploid genome : Xenopus laevis
chipseq
alignment
xenopus
ploidy
6 days ago by
William
▴ 10
0
votes
0
replies
152
views
Differential (pathways) expression testing using linear model packages in R (Limma & GSVA)
GSVA
limma
R
6 days ago by
Tadeoye
▴ 30
0
votes
0
replies
129
views
How to quantify the expression of CD45 isoforms from bulk RNA-seq data
isoforms
Salmon
RNA-seq
CD45
6 days ago by
eager_underdog
• 0
0
votes
5
replies
329
views
How can I determine the number of detected genes and detected transcripts/isoforms in a BAM file + GTF file?
rnaseq
scRNA-seq
single-cell
genomics
ngs
updated 5 days ago by
GenoMax
127k • written 6 days ago by
O.rka
▴ 650
0
votes
2
replies
210
views
Processing fastqs generated by inDrop protocol
single-cell
rna-seq
indrop
updated 6 days ago by
Ram
38k • written 6 days ago by
bobbybobbobbo
• 0
1
vote
3
replies
276
views
How to extract/find the actual names of the gene_IDs if they are not fully presented in gtf.file, and link them to the Count.matrix
featureCounts
gtf
RNA-Seq
updated 6 days ago by
GenoMax
127k • written 6 days ago by
Pegasus
▴ 80
0
votes
1
reply
197
views
Circos plot
circos
updated 5 days ago by
Fabio Marroni
★ 3.0k • written 6 days ago by
prs
• 0
0
votes
1
reply
131
views
mpileup2sync
mpileup2sync
population2
updated 6 days ago by
Ram
38k • written 6 days ago by
Hayler Edu
▴ 30
0
votes
0
replies
94
views
Number of gigabases necesary for Iso-seq-PacBio
Iso-seq
RNA-Seq
Alternative-Splicing
PacBio
updated 6 days ago by
Ram
38k • written 6 days ago by
Jesús M
• 0
899 results • Page
2 of 18
Recent Votes
A: circos plot gene expression by RNA-Seq
Create Interval List for Picard CollectRNASeqmetrics
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
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Answer: getTable ignores query ranges
by
Kyle
• 0
The short answer is you can theoretically do this you just need to a) make your SNPs are two base-pairs in length (i.e. add 1 to the end) a…
Answer: Installing rlang version 1.1.0
by
Lluís R.
★ 1.2k
Having a package duplicated means they are at a different `.libPaths()` sites. Check which version is in which directory and directly remov…
Answer: Somatic truth set
by
samuel
▴ 180
I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39
by
Kyle
• 0
Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
Comment: GetBM - GERP conservation score for GRCm39
by
Kyle
• 0
Perfect answer, thanks Ben!
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2
by
vishal.koparde
▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq?
by
lunarskye222
• 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq
by
GenoMax
127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq
by
samuel
▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts?
by
dsull
★ 4.0k
Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
Comment: Protein name in GenBank
by
GenoMax
127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq
by
GenoMax
127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq
by
ATpoint
70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank
by
Mensur Dlakic
★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold
by
ATpoint
70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
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