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122,200 results • Page
653 of 2444
Sort: Rank
Rank
Views
Votes
Replies
1
vote
14
replies
6.7k
views
RNAseq: What is the difference between the units log2 (tpm + 0.001) and log2 (norm_count + 1)
IsoPct
units
RNAseq
4.5 years ago by
muet-10
• 0
1
vote
6
replies
2.8k
views
pheatmap input file
r
Qiime2
pheatmap
4.5 years ago by
Bioinfonext
▴ 480
1
vote
1
reply
3.3k
views
k-mer distribution to estimate the heterozygosity of my assembly
kmer
Assembly
pacbio
purge_dups
updated 4.5 years ago by
kamiljaron
▴ 230 • written 5.0 years ago by
pablo
▴ 350
0
votes
0
replies
777
views
JUM output Splicing events Visualization tools
LeafViz
Leafcutter
JUM
4.5 years ago by
Shashi Kanth
▴ 10
4
votes
4
replies
3.8k
views
How to interpret ScanPy scatter plots for QC filtering?
Python
jupyter-lab
ScanPy
RNA-Seq
scRNA-seq
4.5 years ago by
Pratik
★ 1.1k
1
vote
5
replies
1.8k
views
Variant discordant alignment HISAT2
alignment
HISAT2
RNA-seq
assembly
Galaxy
updated 4.5 years ago by
Diango
• 0 • written 4.5 years ago by
Miquel
• 0
1
vote
2
replies
1.9k
views
Only output SNPs in bcftools
bcftools
SNPs
4.5 years ago by
NewtoBioinfo
• 0
0
votes
3
replies
1.8k
views
Make map file with recombination rate using plink?
germline
plink
updated 4.5 years ago by
4galaxy77
2.9k • written 4.5 years ago by
curious
▴ 900
1
vote
2
replies
1.8k
views
STAR aligner fatal error
mapping
STAR
nanopore
updated 4.5 years ago by
MohammadAlkadi
▴ 70 • written 4.5 years ago by
m.wlodarczyk214
• 0
0
votes
6
replies
68k
views
Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
R
heatmap
error
updated 4.5 years ago by
Abdul Aziz
• 0 • written 6.7 years ago by
luzglongoria
▴ 50
0
votes
1
reply
1.4k
views
Job:
Bioinformatician
genetics
python
java
php
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
Paulo
• 0
0
votes
4
replies
1.7k
views
how to plot one-dimeson heatmap using R
R
heatmap
updated 4.5 years ago by
Alex Reynolds
36k • written 4.5 years ago by
szp770
▴ 10
10
votes
6
replies
5.9k
views
6 follow
Is there a tool to draw local ancestry plots per chromosome?
ideogram
ancestry
lamp-ld
updated 3.3 years ago by
Ram
45k • written 10.0 years ago by
bibb77
▴ 90
5
votes
7
replies
2.0k
views
Creating numbered gene sets from a list of genes
Bash
awk
geneset
updated 4.5 years ago by
cpad0112
21k • written 4.5 years ago by
storm1907
▴ 30
0
votes
1
reply
936
views
Counting column values before Fisher's test ends with NULL in R
statistics
NGS
R
updated 4.5 years ago by
zx8754
12k • written 4.5 years ago by
storm1907
▴ 30
4
votes
6
replies
2.8k
views
Cons of Smith-Waterman Alignment
Smith-Waterman
Genomics
Alignment
DNA
Sequences
updated 4.5 years ago by
German.M.Demidov
★ 3.0k • written 4.5 years ago by
Student
▴ 30
0
votes
0
replies
874
views
Tajima'S D for targeted sequencing data
DnaSP
SNPs
SnpPanel
angsd
TajimaD
4.5 years ago by
meg.nat86
• 0
1
vote
0
replies
1.1k
views
Can you generate a mappability mask with STAR (or another splice-aware aligner)?
STAR
mappability
SNPable
bwa
4.5 years ago by
mercerf93
▴ 10
0
votes
0
replies
891
views
Focused pathway analysis
fgsea
clusterProfiler
GSEA
KEGG
pathway
4.5 years ago by
cwwong13
▴ 40
0
votes
8
replies
1.7k
views
Assembly copy from subdirectory
Assembly
updated 4.5 years ago by
cpad0112
21k • written 4.5 years ago by
Jecy J
• 0
8
votes
6
replies
5.7k
views
How tximport work with gencode transcripts?
RNA-Seq
R
updated 4.3 years ago by
Kevin Blighe
★ 90k • written 7.4 years ago by
Sharon
▴ 610
0
votes
2
replies
3.2k
views
Generating a background file to be used by Homer for motif identification
homer
4.5 years ago by
gkunz
▴ 30
9
votes
5
replies
2.9k
views
How to plot "Distribution of SNPs per Mbp"
plot
updated 4.5 years ago by
Alex Reynolds
36k • written 4.5 years ago by
Curls
▴ 40
5
votes
9
replies
2.4k
views
For loop for MUMmer
shell
bash
forloop
updated 4.5 years ago by
cpad0112
21k • written 4.5 years ago by
AP
▴ 80
2
votes
2
replies
1.4k
views
Problem setting blastdb in linux
blastdb
blastall
updated 4.5 years ago by
Mensur Dlakic
★ 30k • written 4.5 years ago by
blur
▴ 280
0
votes
0
replies
818
views
Ccle miRna data units
Ccle
Mirna-seq
4.5 years ago by
Nihanth
• 0
2
votes
4
replies
1.6k
views
Batch Effect
r
RNA-seq
updated 4.5 years ago by
Matina
▴ 250 • written 4.5 years ago by
pinheirofabiano
▴ 130
0
votes
1
reply
1.6k
views
How to plot LD decay per chromosome
LDdecayplot
LDdecay
updated 4.5 years ago by
natasha.sernova
★ 4.0k • written 4.5 years ago by
Curls
▴ 40
2
votes
1
reply
986
views
Can anyone please tell me whether I should go for multivariable analysis with my data in this condition?
statistics
multivariate
updated 4.5 years ago by
Arsenal
▴ 160 • written 4.5 years ago by
deep771992chanda
▴ 40
1
vote
2
replies
1.1k
views
RNA-seq Normalisation methods to compare using raw miRNA data
miRNA
RNA-seq
normalisation
4.5 years ago by
raavi21198
▴ 20
0
votes
4
replies
2.4k
views
struct.error in MACS2 callpeak
ChIP-seq
MACS2
4.5 years ago by
ty0017
• 0
0
votes
0
replies
1.2k
views
HaplotypeCaller run time ?
WGS
Haplotypecaller
GATK
4.5 years ago by
quentin54520
▴ 120
2
votes
4
replies
1.8k
views
Close homologs search
search
BLAST
homologs
updated 4.5 years ago by
Mensur Dlakic
★ 30k • written 4.5 years ago by
Vladimir Leshuk
▴ 50
0
votes
4
replies
4.6k
views
High Sierra vs Catalina vs Big Sur
MAC
OS
4.4 years ago by
ddraki2008
• 0
0
votes
0
replies
1.1k
views
Misunderstanding on calculating Ka/Ks values
Nucleotide
4.5 years ago by
Abdukhalim Khon
• 0
6
votes
13
replies
9.1k
views
Choosing a high soft thresholding power in WGCNA, is it reasonable?
WGCNA
updated 4.4 years ago by
andres.firrincieli
3.9k • written 4.6 years ago by
aristelliger
▴ 10
0
votes
0
replies
753
views
Where to find hepatitis virus infectious status information available in TCGA or ICGC database when study HCC?
manipulation
HCV
clincal
data
HCC
ICGC
3.2 years ago by
Dude
• 0
1
vote
8
replies
5.4k
views
6 follow
DESeq2 count matrix read in
deseq2
R
updated 2.7 years ago by
Ram
45k • written 4.5 years ago by
Gregor Rot
▴ 550
0
votes
0
replies
634
views
Need help contig assembly
Contig
updated 4.5 years ago by
Ram
45k • written 4.5 years ago by
saingamp
• 0
2
votes
3
replies
1.6k
views
MACS2 does not giving same result before and after chromosome extraction from bam file
chromosome
samtools
extract
peakcalling
macs2
updated 4.5 years ago by
seidel
11k • written 4.5 years ago by
buffealo
▴ 130
0
votes
0
replies
1.5k
views
findMotifs vs findMotifsGenome, inequality of results
homer
motifs
4.5 years ago by
boczniak767
▴ 880
10
votes
13
replies
9.4k
views
snp density plot
snp
updated 4.5 years ago by
Curls
▴ 40 • written 6.1 years ago by
evelyn
▴ 230
9
votes
11
replies
6.3k
views
BED file: Find intervals that overlap a certain percentage and keep the longest one
Bed
bedtools
bash
bedops
4.5 years ago by
biomonte
▴ 220
1
vote
0
replies
1.1k
views
Job:
Senior Bioinformatician in Molecular Screening and Omics Research - AstraZeneca, Cambridge, UK
omics
screening
AstraZeneca
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
Sergio Martínez Cuesta
▴ 230
0
votes
2
replies
1.7k
views
What is current the best available rat lung single cell RNA seq dataset for cell type annotation? any recommendations ?
SingleR
scRNAseq
4.5 years ago by
FantasticAI
▴ 60
0
votes
1
reply
2.8k
views
IGV not showing transcripts
transcripts
IGV
updated 4.5 years ago by
ATpoint
90k • written 4.5 years ago by
shaden
▴ 20
0
votes
0
replies
864
views
How can I convert a molecule written in SMILE in SMART?
superimposition
ligands
open_babel
4.5 years ago by
Agnese
• 0
1
vote
1
reply
1.4k
views
Homer motif analysis
Homer
R
motif
updated 4.5 years ago by
seidel
11k • written 4.5 years ago by
Rorey
• 0
0
votes
4
replies
3.7k
views
KaKs calculator
Nucleotide
Substitutions
updated 4.3 years ago by
Elaine Wang
• 0 • written 4.5 years ago by
Abdukhalim Khon
• 0
1
vote
0
replies
988
views
How does FDRtool work?
rnaseq
fdrtool
deseq2
r
pvalue
4.5 years ago by
emmagervide
▴ 10
122,200 results • Page
653 of 2444
Recent Votes
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
Converting GFF to GTF
Answer: best practice for diploid variant calling
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Can i use orthofinder for small protein datasets and not full proteome?
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Recent Replies
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 10
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
▴ 10
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…
Comment: Can i use orthofinder for small protein datasets and not full proteome?
by
alexandrakortsi
• 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
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…
Comment: Subsetting before QC in Spatial Transcriptomics
by
Kent
▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around
by
Luca Arbore
▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets
by
GenoMax
154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets
by
DrSmad
▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types
by
shpak.max
▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets
by
GenoMax
154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat
by
yura.grabovska
▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays
by
yura.grabovska
▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
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