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1,000 results • Page
4 of 20
Sort: replies
Rank
Views
Votes
Replies
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter
genome
updated 11 months ago by
Ram
43k • written 4.6 years ago by
Kumar
▴ 120
1
vote
8
replies
2.5k
views
Using NCBIs EDirect to download pubmed abstract
edirect
pubmed
NCBI
updated 10 months ago by
Ram
43k • written 5.8 years ago by
zorn21g
• 0
2
votes
8
replies
693
views
TCGA Biospecimens Slides Extraction
tcga
updated 9 weeks ago by
Zhenyu Zhang
★ 1.2k • written 10 weeks ago by
jain72744
▴ 10
3
votes
8
replies
2.0k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 11 months ago by
Ram
43k • written 5.5 years ago by
nagendranp1991
• 0
4
votes
8
replies
1.9k
views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE …
super-enhancers
Enhancers
updated 3 months ago by
jared.andrews07
★ 16k • written 3 months ago by
Manhezz
• 0
0
votes
8
replies
1.3k
views
Creating fastq subsets from existing files
scRNA-seq
umi_tools
cellranger
fastq
8 months ago by
Zack
• 0
2
votes
8
replies
1.0k
views
VCF file CSQ flag
vcf
exome-sequencing
updated 10 months ago by
Ram
43k • written 10 months ago by
Payal
▴ 160
1
vote
8
replies
1.5k
views
counts of cite-seq-count vs. cellrenager varies tremendously
citeseq-count
cellranger
cite-seq
scRNA-seq
updated 4 months ago by
ATpoint
82k • written 9 months ago by
Assa Yeroslaviz
★ 1.8k
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 13 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
0
votes
8
replies
656
views
Phobius error: Could not read provided fasta sequence at phobius.pl line 408
Phobius
updated 8 weeks ago by
ido.idobar
▴ 10 • written 3 months ago by
Elizabeth
▴ 30
0
votes
8
replies
1.9k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython
python
updated 10 months ago by
Ram
43k • written 4.4 years ago by
muhammad.khizerkiet
• 0
0
votes
8
replies
343
views
Error in cnetplot enrichplot package
R
updated 7 days ago by
Ram
43k • written 7 days ago by
Farhad
• 0
5
votes
8
replies
607
views
Multiple threads on ubuntu server
Ubuntu
updated 3 months ago by
colindaven
6.4k • written 3 months ago by
oghzzang
▴ 50
5
votes
8
replies
1.9k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq
DNA-Seq
contamination
QC
updated 6 months ago by
Jingjingzhang
• 0 • written 3.7 years ago by
from the mountains
▴ 230
3
votes
8
replies
2.0k
views
Kallisto mapping paired end
Kallisto
mapping
updated 11 months ago by
Ram
43k • written 2.2 years ago by
Dk
▴ 20
1
vote
8
replies
3.9k
views
No gene can be mapped
R
GSEA
updated 4 months ago by
jv
★ 1.8k • written 2.3 years ago by
yang.zhizhang
• 0
1
vote
8
replies
383
views
Downsampling fastq file
downsample
fastq
1 hour ago by
marco.barr
▴ 80
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 8 months ago by
Ram
43k • written 8.0 years ago by
nikelle.petrillo
▴ 110
1
vote
8
replies
1.1k
views
How does one access TCGA controlled data in AWS S3?
tcga
aws
updated 6 months ago by
Zhenyu Zhang
★ 1.2k • written 6 months ago by
Cmouli
▴ 10
0
votes
8
replies
1.5k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools
MarkDuplicates
updated 6 weeks ago by
xiangbinruan
• 0 • written 19 months ago by
Phoebe Magdy
• 0
0
votes
8
replies
568
views
STAR aligner options
STAR
4 weeks ago by
theophile
• 0
6
votes
8
replies
1.2k
views
conda: command not found: gatk.
conda
gatk
10 months ago by
bestone
▴ 30
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq
deseq2
updated 10 months ago by
Ram
43k • written 3.9 years ago by
kand3e
▴ 60
4
votes
8
replies
1.8k
views
Error while running nf-core/rnaseq pipeline
nf-core
RNA-seq
11 months ago by
eesha28112001
• 0
3
votes
8
replies
991
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST
bowtie2
BWA
alignment
8 months ago by
cheesefish21
▴ 10
0
votes
8
replies
1.2k
views
BAM header edit with a list of amplicons
samtools
BAM
updated 10 months ago by
Ram
43k • written 2.3 years ago by
ltalignani
• 0
2
votes
8
replies
984
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 9 weeks ago by
bharata1803
▴ 560 • written 4 months ago by
LauferVA
4.2k
0
votes
8
replies
1.5k
views
VCF samtools
vcf
samtools
variant-calling
updated 10 months ago by
Ram
43k • written 2.4 years ago by
Lucía
• 0
5
votes
8
replies
2.4k
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
updated 9 months ago by
Jordan M Eizenga
▴ 460 • written 15 months ago by
TN
• 0
2
votes
7
replies
856
views
Should we assume UMI-based scRNAseq data is not compositional?
compositional
scRNAseq
9 months ago by
cwwong13
▴ 40
2
votes
7
replies
1.8k
views
Technology Stack of NCBI (Genbank, GEO, etc.)
sequence
ncbi
gene
genbank
updated 11 months ago by
Ram
43k • written 6.2 years ago by
navela78
▴ 70
0
votes
7
replies
413
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 25 days ago by
Papyrus
★ 2.9k • written 26 days ago by
doramora
▴ 10
0
votes
7
replies
925
views
Mugsy error -directory must be a directory
Mugsy
updated 7 months ago by
Ram
43k • written 3.4 years ago by
A_heath
▴ 160
0
votes
7
replies
1.9k
views
monocle single cell differential expression: error message for HSMM <- estimateDispersions(HSMM) command
single-cell
monocle
updated 9 months ago by
benformatics
3.9k • written 2.3 years ago by
bioinformatics
▴ 40
6
votes
7
replies
573
views
NF-Core ampliseq - Rscript markdown error
nf-core
ampliseq
updated 3 months ago by
Michael
54k • written 3 months ago by
nermze
• 0
0
votes
7
replies
458
views
1000 Genome: Cause of duplicate variants with different genotypes
CrossMap
1000Genome
1000G
updated 11 weeks ago by
Giulio Genovese
▴ 390 • written 11 weeks ago by
JourneyToAbyss
▴ 210
3
votes
7
replies
6.4k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 11 months ago by
DareDevil
★ 4.3k • written 6.3 years ago by
win
▴ 970
0
votes
7
replies
1.6k
views
Comparing the GVF file & VCF file
gvf
dna
vcf
ensembl
ngs
updated 5 months ago by
mickeykuo129
• 0 • written 15 months ago by
Alireza
▴ 30
0
votes
7
replies
1.2k
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 11 months ago by
LauferVA
4.2k • written 11 months ago by
Camilo Andres
▴ 40
0
votes
7
replies
3.8k
views
MUMmer plot visualization
MUMmer plot
updated 10 weeks ago by
Carlos
• 0 • written 3.2 years ago by
rthapa
▴ 90
0
votes
7
replies
440
views
Error "ckalloc: request for negative space" about multiz
multiz
8 weeks ago by
marh32
• 0
4
votes
7
replies
1.0k
views
Statistical test to compare data across timepoints
Statistics
updated 6 months ago by
Matthias Zepper
4.6k • written 6 months ago by
Sean
▴ 20
2
votes
7
replies
559
views
Need a link to OLDERADO server
pdb
protein
nmr
structure
6 weeks ago by
b2003
• 0
1
vote
7
replies
1.5k
views
Typical percentage of multimapping reads in human rna-seq?
RNA-seq
alignment
Bowtie2
STAR
updated 10 months ago by
GenoMax
141k • written 10 months ago by
srhic
▴ 60
6
votes
7
replies
1.7k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters
Algorithm
Software
updated 11 months ago by
Ram
43k • written 6.9 years ago by
nilo
▴ 90
0
votes
7
replies
7.2k
views
Problem in in alignment by muscle
sequence
muscle
alignment
updated 10 months ago by
Ram
43k • written 6.7 years ago by
misbahabas
▴ 70
3
votes
7
replies
2.6k
views
6 follow
Online BLAST search using R
BLAST
R
updated 10 weeks ago by
SequenceServer
▴ 140 • written 2.7 years ago by
accibio
▴ 20
0
votes
7
replies
578
views
Trying to extract .cram file read sequences into array
CRAM
pysam
reads
samtools
9 weeks ago by
sacryt
• 0
0
votes
7
replies
386
views
single nuclei sequencing questions
fastq
single-nuclei-sequencing
updated 7 weeks ago by
Ram
43k • written 7 weeks ago by
Long
• 0
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT
TF-footprinting
ATAC-seq
updated 10 months ago by
Ram
43k • written 5.4 years ago by
grant.hovhannisyan
★ 2.6k
1,000 results • Page
4 of 20
Recent Votes
CTO/founding engineer role at Voyant Bio
Programmatically retrieving positions of protein active site residues
Programmatically retrieving positions of protein active site residues
A: Can Biopython Properly Import Fasta Headers With Spaces In Them?
Programmatically retrieving positions of protein active site residues
Answer: Polishing genome assembly
Answer: Integrate transcriptomic data and proteomics data.
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Recent Replies
Comment: KEGG Pathways
by
Ram
43k
Give us as much detail as you can. What error does it give you?
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
SRA Run Selector shows a better view of the metadata: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA761679&o=acc_s%3Aa
Comment: Adjust pvalue in R with different approach give me all different outcome
by
Aspire
▴ 300
- p.adjust() is supposed to receive a **numeric vector of p-values**, not a matrix. - It makes no sense to "adjust" just one p-value, as…
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I understood where the problem lies. I discussed with my wet lab colleagues (this is part of a bioinformatician's job...) and by showing th…
Comment: Programmatically retrieving positions of protein active site residues
by
me
▴ 760
This question fits in nicely with the [SIB Swiss Institute of Bioinformatics course on Enzyme information in UniProt][1] [1]: https://w…
Answer: Programmatically retrieving positions of protein active site residues
by
me
▴ 760
This can be done via SPARQL at the UniProt.org sparql endpoint PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX fald…
Comment: KEGG Pathways
by
Sudip
• 0
No it does not. Do you know of a way that can help me achieve what I want?
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
by
GenoMax
141k
UniRef file is 43G compressed so probably will become ~60G when uncompressed. You would likely be looking at at least that much +10-20% GB …
Comment: RNAseq one control two conditions, shared and exclusive genes
by
matteo.levorato
• 0
thank you for your comment, but yes running DESeq2 is the starting point. dds <- DESeqDataSetFromMatrix(countData=RawCounts, …
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
by
Ram
43k
Please stop pasting a sentence in the `tags` field. That field is for subject matter keywords. I've fixed your posts this time, please be m…
Comment: KEGG Pathways
by
Ram
43k
> is the below code correct Does it give you what you need?
Comment: from row count to tpm
by
Ram
43k
Hi https://www.biostars.org/u/119503/ Why did you delete this post?
Comment: ERROR When Using Ensembl Plants Biomart Wget API
by
GenoMax
141k
A couple of hours back using `plants.ensembl.org` was generating a 504 error but it seems to be working now. wget -O result.txt 'http…
Comment: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
Don't understand this comment. I don't have any columns with this name.
Answer: ERROR When Using Ensembl Plants Biomart Wget API
by
Ben_Ensembl
★ 2.4k
Hi Dora, For plant species such as *A. thalina*, you should use the http://plants.ensembl.org/biomart service, so the start of your wget…
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