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122,202 results • Page
675 of 2445
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Votes
Replies
0
votes
1
reply
4.4k
views
How to increase the size of the top annotation bars in Complexheatmap
plot
annotation
ComplexHeatmap
heatmap
4.6 years ago by
mohammedtoufiq91
▴ 270
0
votes
2
replies
1.9k
views
How to produce overlapping QQ-plot from GWAS results?
R
data-visalization
GWAS
SNP
4.6 years ago by
anikcropscience
▴ 270
1
vote
8
replies
5.6k
views
XGBoost on the unbalanced data
unbalanced_data
4.6 years ago by
mrashad
▴ 80
5
votes
5
replies
3.7k
views
How to remove all-N sequence entries from fasta file.
awk
perl
updated 4.6 years ago by
cpad0112
21k • written 4.6 years ago by
Info.shi
▴ 30
0
votes
1
reply
661
views
Inserting N bases at 5' end of clipped reads
GenomicAlignments
Samtools
cutadapt
Bowtie2
updated 4.6 years ago by
Pierre Lindenbaum
166k • written 4.6 years ago by
joshrennick.1
• 0
2
votes
6
replies
4.2k
views
for loop to filter dataframe based on conditions
r
loop
filter
4.6 years ago by
katinstack
• 0
0
votes
0
replies
904
views
Plink2: Determine if allele2 is major or ref
plink2
plink
4.6 years ago by
Brynjar
▴ 20
0
votes
0
replies
700
views
How to correctly map CORALL-generated RNA-seq data to a reference genome?
CORALL
stranded
mapping
paired-end
RNA-seq
4.6 years ago by
niklasjoshua.ebner
• 0
3
votes
7
replies
3.0k
views
Can too high of a ChIPQC RiP% be indicative of insufficient stringency in peak calling?
R
ChIP-seq
ChIPQC
updated 4.6 years ago by
dariober
15k • written 4.6 years ago by
gkunz
▴ 30
2
votes
1
reply
1.6k
views
RPKM and FPKM quality control check and filtration
scRNA-Seq
updated 4.6 years ago by
Bastien Hervé
6.5k • written 4.6 years ago by
sunshine
• 0
1
vote
3
replies
1.9k
views
Lower bound of y-axis hidden in UpSet plot in R, how to avoid this
Plot
R
UpSet
updated 4.6 years ago by
ATpoint
90k • written 4.6 years ago by
Søren
• 0
0
votes
3
replies
3.7k
views
No GO-term and no ontology in goseq() output! What am I doing wrong?
goseq
GO-term
ontology
test.cats
updated 3.8 years ago by
Ram
45k • written 11.1 years ago by
Parham
★ 1.6k
0
votes
2
replies
1.4k
views
Protein Ligand Docking Software Suggestion
Docking
software
4.6 years ago by
Qinqing
• 0
0
votes
3
replies
2.7k
views
beagle error: genotype is missing allele separator
imputation
genomics
updated 4.4 years ago by
Ram
45k • written 4.6 years ago by
ziv_attia
• 0
15
votes
15
replies
14k
views
Single cell RNA-seq: how many PCs to use for t-SNE/UMAP?
umap
pca
scRNA-seq
t-sne
RNA-seq
4.6 years ago by
MutationalMeltdown
▴ 200
1
vote
2
replies
1.8k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNAseq
AnnotationDbi
updated 4.6 years ago by
rodolfo.peacewalker
▴ 390 • written 4.6 years ago by
Ezequiel
• 0
1
vote
5
replies
2.2k
views
Blastn in galaxy
Blastn
galaxy
updated 20 months ago by
Ram
45k • written 4.6 years ago by
adnan.lahuf
• 0
6
votes
12
replies
5.5k
views
7 follow
Multiqc raises the "cannot import name 'gcd' from 'fractions'" error
multiqc
linux
rna-sq
updated 4.6 years ago by
Phil Ewels
★ 1.5k • written 4.6 years ago by
sabbirakhand25
• 0
0
votes
5
replies
1.7k
views
How to filter reads only with single SNV
filtering_reads
SNV
amplicon_sequencing
SNP
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
sunhyunchang
• 0
0
votes
4
replies
1.6k
views
Bioinformatics researcher looking for an answer on edgeR and DESeq2
rna-seq
R
edgeR
gene
updated 4.6 years ago by
EagleEye
7.6k • written 4.7 years ago by
skmhabeeb
• 0
3
votes
0
replies
1.0k
views
Using bulk RNA-seq deconvolution as covariates in bulk RNA-seq differential expression analysis
cibersort
dwls
deconvolution
4.6 years ago by
telroyjatter
▴ 240
0
votes
0
replies
1.0k
views
How to produce multiple sequence alignment figures with phenotypic data?
alignment
multiple-alignment
sequence
4.6 years ago by
anikcropscience
▴ 270
4
votes
5
replies
2.2k
views
6 follow
Looking for a Whole Genome Sequencing GrCH38 Control group of roughly 250 samples
wgs
control
whole
updated 4.6 years ago by
4galaxy77
2.9k • written 4.6 years ago by
screadore
▴ 20
0
votes
1
reply
2.6k
views
how to run and use the ENCODE ATAC-seq pipline
ATAC-seq
ENCODE
peak
updated 4.6 years ago by
Jeremy Leipzig
23k • written 4.7 years ago by
cwwong13
▴ 40
4
votes
4
replies
2.0k
views
htseq-count Error '_StepVector_Iterator_obj' object has no attribute 'next'
htseq-count
updated 4.0 years ago by
mlist2014
• 0 • written 4.6 years ago by
Sara
▴ 20
1
vote
1
reply
1.3k
views
Rare cell population in single cell ATAC-Seq
atac-seq
atac
updated 4.6 years ago by
heskett
▴ 110 • written 4.6 years ago by
ahmad mousavi
▴ 800
0
votes
1
reply
1.6k
views
How to get GSE data into IGV
ChIP-Seq
IGV
GSE
updated 4.6 years ago by
heskett
▴ 110 • written 4.6 years ago by
michael.laz
• 0
0
votes
8
replies
2.5k
views
Split fasta based on symbol and numeric position in header
python
fasta
sequence
genome
split
4.6 years ago by
Nick Scales
• 0
0
votes
0
replies
817
views
Detecting mono-allelic expression in RNA-seq in human
binomial
allele_specific
gene_expression
rna-seq
4.6 years ago by
heskett
▴ 110
4
votes
4
replies
2.2k
views
Is Biopython a Package or Library?
Biopython
Python
updated 3.0 years ago by
Ram
45k • written 4.6 years ago by
anasjamshed
▴ 140
2
votes
2
replies
1.2k
views
Genes with identical reads mapping values across all samples - Kallisto
gene
Kallisto
expression
updated 4.6 years ago by
Michael
56k • written 4.6 years ago by
andres.firrincieli
3.9k
0
votes
0
replies
924
views
Compare segment data produced by CopywriteR and similar tools
copywriter
cna
4.6 years ago by
Ram
45k
1
vote
1
reply
749
views
R libraries to match SNPs by positions (including switching and flipping)
R
Bioconductor
SNP
updated 4.6 years ago by
Ram
45k • written 4.6 years ago by
timing
▴ 20
3
votes
2
replies
1.2k
views
Is anticancer action of HDAC inhibitors - cancer cells specific or it may cause death to other cell types ?
cancer
updated 4.6 years ago by
Jean-Karim Heriche
27k • written 4.6 years ago by
Alexander
▴ 220
0
votes
0
replies
707
views
How to incorporate the GRM into a mixed linear model
gwas
GRM
animal_model
4.6 years ago by
DIMITRIOS
• 0
0
votes
0
replies
2.1k
views
Job:
Group Leader Computational Cancer Biology - VIB-KU Leuven, Belgium
vib
groupleader
cancer
biology
computational
4.6 years ago by
leen.notebaert
• 0
0
votes
4
replies
1.8k
views
sequence similarity
blast
linux
fasta
updated 4.6 years ago by
Joe
22k • written 4.6 years ago by
lorenzinip
• 0
0
votes
3
replies
3.7k
views
Tassel5v2 vcf file with 'N' in reference and alternate allele
Tassel5v2
SNPcalling
GBS
updated 4.6 years ago by
Lindsay
• 0 • written 6.1 years ago by
Tm
★ 1.1k
0
votes
0
replies
762
views
Calculate accuracy for a Cox model in R
accuracy
cox
prediction
survival
R
4.6 years ago by
nolwenn
▴ 10
0
votes
0
replies
759
views
News:
Online Training - Microbial Metabarcoding - 4-8 October
MicrobialEcology
metabarcoding
updated 4.4 years ago by
Ram
45k • written 4.6 years ago by
Physalia-courses
★ 2.7k
1
vote
2
replies
1.5k
views
DEG list turn into keggscape
Cytoscape
RNA-Sequencing
4.6 years ago by
ashwing.kofficial
▴ 10
0
votes
5
replies
2.8k
views
How to calculate bam coverage apart from Qualimap?
bam
qualimap
coverage
4.6 years ago by
marongiu.luigi
▴ 770
0
votes
0
replies
896
views
Interpreting partial dependence plots
machinelearning
caret
partialdependenceplot
pdp
R
4.6 years ago by
fana
▴ 40
1
vote
1
reply
1.7k
views
Do I need to assume differences in coverage profile when I compare the first reads from paired end data with single end read data?
single-end
paired-end
sequencing
mapping
coverage
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
corinna.ernst
• 0
5
votes
8
replies
2.9k
views
Loading PCA - different value depending on the package used
factormineR
PCAtools
pca
prcomp
loadings
updated 4.6 years ago by
Kevin Blighe
★ 90k • written 4.6 years ago by
camillab.
▴ 160
0
votes
3
replies
1.6k
views
Gigabase Clarification (Same as Gigobyte?)
genomics
4.6 years ago by
joe_genome
▴ 70
1
vote
4
replies
2.3k
views
Create Mutational signature plot from vcf file.
R
python
mutational
4.6 years ago by
nhaus
▴ 420
2
votes
1
reply
2.1k
views
Why bamToFastq returns empty fastq files?
bamToFastq
error
bam
fastq
updated 4.6 years ago by
ATpoint
90k • written 4.6 years ago by
marongiu.luigi
▴ 770
0
votes
2
replies
991
views
16S Barcoding long and short sequences return different BLAST results
barcoding
16S
4.6 years ago by
robert.murphy
▴ 110
0
votes
0
replies
1.0k
views
how to sort out regions with corresponding scores using computematrix?
computematrix
deeptools
plotheatmap
4.6 years ago by
jiekwo1
• 0
122,202 results • Page
675 of 2445
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Comment: Visualize methylation status in Pacbio Hifi read
by
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★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
• 0
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
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Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
• 0
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
samuel.a.odonnell
▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets
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zizigolu
★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
Pierre Lindenbaum
166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
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by
alexandrakortsi
• 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
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xinguok794
▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
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Kent
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Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
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by
Luca Arbore
▴ 10
Thank you very much Kevin, it worked!
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