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122,200 results • Page
656 of 2444
Sort: Rank
Rank
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Votes
Replies
1
vote
7
replies
4.1k
views
bbduk trimmed out too many sequences
bbduk
bbmap
amplicon
updated 4.5 years ago by
GenoMax
154k • written 4.5 years ago by
AfinaM
▴ 30
0
votes
2
replies
2.3k
views
How to grep fasta sequence using list of IDs
grep
FASTA
Sequence
4.5 years ago by
Kumar
▴ 170
4
votes
1
reply
1.0k
views
R script for Gene ID Mapping?
mapping
R
IDmapping
geneID
updated 4.5 years ago by
Ram
45k • written 4.5 years ago by
shrgur
• 0
0
votes
2
replies
886
views
Looking for a user-friendly comparative genomics program
comparative
genomics
updated 4.5 years ago by
GenoMax
154k • written 4.5 years ago by
kira kira
• 0
41
votes
20
replies
42k
views
12 follow
output TMM normalized counts with edgeR
differential expression
RNA-Seq
updated 3.6 years ago by
N.
• 0 • written 7.5 years ago by
guillaume.rbt
★ 1.0k
1
vote
2
replies
5.2k
views
CPM or pesudo.counts, which is the normalized counts
edgeR, CPM
edgeR
cpm
pesudo.counts
updated 4.5 years ago by
shengxin1015
▴ 10 • written 10.0 years ago by
lilingjoyo
▴ 40
0
votes
5
replies
2.7k
views
the fixed-effects model matrix is column rank deficient when adding a variable
voom
LIMMA
dream
RNA
rescale
updated 4.5 years ago by
Shab86
▴ 310 • written 4.5 years ago by
Will
▴ 20
4
votes
4
replies
2.7k
views
Extracting reads from BAM file based on partial read name
BAM
CLI
picard
RNA-Seq
updated 4.5 years ago by
seidel
11k • written 4.5 years ago by
julianneradford
▴ 20
2
votes
3
replies
2.0k
views
Deleterious or Protective? --> CADD score >20 but Odds ratio <1
variant
deleteriousness
genomics
updated 4.5 years ago by
Kevin Blighe
★ 90k • written 4.5 years ago by
Shab86
▴ 310
1
vote
3
replies
1.2k
views
Help with record.id
pyrosetta
python
biopython
updated 2.7 years ago by
Ram
45k • written 4.5 years ago by
Maya
• 0
3
votes
5
replies
2.3k
views
how can I turn a skinny/long data frame into a Seurat object
sparse-matrix
seurat
scrna-seq
4.5 years ago by
glocke01
▴ 190
2
votes
14
replies
3.1k
views
Genetic Variants in NGS analysis
variants
NGS
4.5 years ago by
sarastrafella.ss
▴ 20
0
votes
0
replies
718
views
Batch Effects in Multiplexed Perturbations
demultiplexing
cellhashing
singlecell
scRNAseq
4.5 years ago by
fouerghi20
▴ 90
0
votes
2
replies
985
views
VennDiagram for differentially expressed proteins
proteomics
VennDiagram
4.5 years ago by
yannick.venturaavila
• 0
7
votes
4
replies
7.8k
views
scvelo vs velocyto
velocyto
python
scvelo
updated 3.8 years ago by
Friederike
9.0k • written 4.5 years ago by
Jeffrey3555054
▴ 20
0
votes
5
replies
2.3k
views
FeatureCounts error
RNAseq
updated 4.5 years ago by
ATpoint
90k • written 4.5 years ago by
m.wlodarczyk214
• 0
0
votes
1
reply
928
views
Variable name shuffles in Correlation Plot in R
R
Biostatistics
Corrplot
Correlation
updated 4.5 years ago by
cpad0112
21k • written 4.5 years ago by
jansha.1997
• 0
0
votes
1
reply
727
views
Gene name according to assembly
hg38
genome
assembly
name
hg18
updated 4.5 years ago by
GenoMax
154k • written 4.5 years ago by
GG
• 0
2
votes
4
replies
2.7k
views
hg18, hg19, hg38
hg38
hg19
genome
assembly
hg18
updated 4.5 years ago by
GenoMax
154k • written 4.5 years ago by
GG
• 0
1
vote
2
replies
2.8k
views
Remove sites with heterozygote excess with VCFtools
SNPs
genomics
VCFTools
hetexcess
4.5 years ago by
Konstantinos
• 0
0
votes
2
replies
1.4k
views
How do commercially NIPT tests work?
NIPT
NGS
Defrag
WisecondorX
Sanefalcon
updated 4.5 years ago by
German.M.Demidov
★ 3.0k • written 5.3 years ago by
Lucas
▴ 20
0
votes
0
replies
646
views
Prediction model in R
Prediction
R
Rstudio
model
4.5 years ago by
yura.10.08.94.94
• 0
0
votes
0
replies
828
views
Tool/server for metal ion amino acid binding site prediction ?
proteomics
database
python
genomics
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
Kumar
▴ 120
2
votes
1
reply
1.6k
views
Error with SRA Toolkit prefetch command
timeout
sra
ncbi
https
updated 4.5 years ago by
ATpoint
90k • written 4.5 years ago by
elisheva
▴ 120
4
votes
3
replies
3.7k
views
Gold standard for bulk RNA-seq downsampling - number of uniquely mapped reads
uniquely
RNA-seq
mapping
bulk
downsampling
4.5 years ago by
msimmer92
▴ 310
0
votes
0
replies
601
views
Selective sweep for scaffold level reference genome
positiveselection
denovo
selectivesweep
scaffold
4.5 years ago by
Mel Kile
• 0
1
vote
4
replies
1.7k
views
What is the advantage of having BAM files per sample compared to one BAM file containing all samples?
NGS
BAM
SNPcalling
4.5 years ago by
L_to_the_m
▴ 10
1
vote
9
replies
2.1k
views
Can anyone please name this tool to make a genome map?
graphics
genome
updated 4.5 years ago by
Ram
45k • written 4.5 years ago by
zack.saud
▴ 50
0
votes
5
replies
1.7k
views
Problem creating a reference genome
reference
custom
genome
4.5 years ago by
lydiaiglesias
• 0
1
vote
7
replies
16k
views
A problem with download SRA using SRA toolkit
SRAtoolkit
NCBI
SRA
updated 2.4 years ago by
Ram
45k • written 5.8 years ago by
reza
▴ 300
0
votes
1
reply
782
views
genbank output incomplete with long feature name
biopython
SeqFeature
genbank
SeqIO
updated 4.5 years ago by
Joe
22k • written 4.5 years ago by
QL
• 0
0
votes
2
replies
1.1k
views
extract reference and query coordinate from bam or sam file
sam
bam
4.5 years ago by
LMoon
• 0
0
votes
0
replies
925
views
Fully online, single modules/courses in Bioinformatics and Omics Data Analysis?
university
omics
online
academic
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
lorenzo.fabbri92sm
• 0
0
votes
3
replies
1.6k
views
Help! Master regulator prediction from DEGs in RNA-seq
GRN
transcription
rna-seq
DEG
transcriptomics
updated 4.5 years ago by
MohammadAlkadi
▴ 70 • written 4.5 years ago by
ngarber
• 0
0
votes
0
replies
2.1k
views
Bismark to MethylKit
methylkit
bismark
bsseq
4.5 years ago by
Arindam Ghosh
▴ 550
1
vote
1
reply
1.1k
views
Compare protein functionality between species
Genetics
Comparative
Proteomics
updated 4.5 years ago by
Mensur Dlakic
★ 30k • written 4.5 years ago by
Howard
• 0
0
votes
4
replies
1.7k
views
I'm having some problems when I calculated PRS by PRsice
PRsice
PRsice-2
error
4.5 years ago by
dong
• 0
0
votes
1
reply
1.1k
views
How to use python to align 30 kb genome to another 30kb reference, repeat 10x times ?
Alignment
reference-alignment
python
updated 4.5 years ago by
WouterDeCoster
48k • written 4.5 years ago by
d.s.account
▴ 10
0
votes
0
replies
660
views
Whole Proteome Alignment
divergence
alignment
proteome
4.5 years ago by
sentionaut
• 0
8
votes
15
replies
9.2k
views
6 follow
blastn error - NCBI C++ Exception
assembly
blast
alignment
updated 3.7 years ago by
lieven.sterck
16k • written 4.7 years ago by
sunnykevin97
▴ 1000
0
votes
0
replies
1.1k
views
Calculating net charge of a ligand.
amber
ligand
Charge
4.5 years ago by
Ammar Danazumi
▴ 10
10
votes
7
replies
6.0k
views
Forum:
Conceptual - Do I need to justify myself if I generate more than three replicates?
statistics
conceptual
4.5 years ago by
c_u
▴ 530
0
votes
1
reply
1.3k
views
Merging Bam Files with Rsamtools
mergeBam
Rsamtools
updated 4.5 years ago by
Ram
45k • written 4.5 years ago by
rbravos87
• 0
0
votes
0
replies
689
views
Chipseq allelic density plot for TSS region
Chip-Seq
Allelic-Chipseq
Deeptools
4.5 years ago by
BISEP
▴ 10
0
votes
2
replies
904
views
Identical BLAST search query producing different results?
BLAST
4.5 years ago by
Felixculpa
• 0
1
vote
1
reply
1.2k
views
Trimming gene coding sequence for finding TFBS
tfbs
transcription
binding
rna-seq
4.5 years ago by
greyman
▴ 190
0
votes
2
replies
1.6k
views
subset of paired end reads from bam file or fastq file of different depth
depth
ShortRead
samtools
read
4.5 years ago by
rthapa
▴ 90
2
votes
3
replies
1.9k
views
Difference between fCDS and CDS
fCDS
CDS
4.5 years ago by
Prashant
▴ 10
0
votes
1
reply
4.0k
views
Editing Seurat object metadata
scRNA-seq
Seurat
snRNA-seq
updated 4.5 years ago by
fracarb8
★ 1.8k • written 4.5 years ago by
LacquerHed
▴ 30
0
votes
1
reply
843
views
Suggestion on parsing multipe alignment in fasta format
mafft
multiple
msa
sequence
clustal
updated 4.5 years ago by
cpad0112
21k • written 4.5 years ago by
QLFblaireau
▴ 30
122,200 results • Page
656 of 2444
Recent Votes
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
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Answer: Getting the overlap between two GTF files
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Recent Replies
Comment: ID unifiying across different datasets
by
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…
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(…
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