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1,113 results • Page
2 of 23
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0
votes
1
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119
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Ruqaiya
• 0
0
votes
1
reply
266
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 1 day ago by
trausch
★ 1.9k • written 18 days ago by
zec018
• 0
0
votes
0
replies
89
views
LEfSe
LEfSe
1 day ago by
benkosta
• 0
0
votes
0
replies
77
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
1 day ago by
Sara
▴ 30
1
vote
4
replies
354
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
1 day ago by
hagl
▴ 10
0
votes
2
replies
165
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
5 hours ago by
matteo.levorato
• 0
0
votes
2
replies
129
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
1 day ago by
Lluís R.
★ 1.2k
0
votes
1
reply
124
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
DOBI
• 0
0
votes
0
replies
89
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
1 day ago by
atharvakarkare14
▴ 20
5
votes
16
replies
607
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
1 day ago by
Ruqaiya
• 0
0
votes
2
replies
174
views
What should I consider as FASTA for dataset?
PDB
FASTA
1 day ago by
Nafi
• 0
37
votes
24
replies
1.7k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 11 hours ago by
i.sudbery
19k • written 3 days ago by
noodle
▴ 580
0
votes
0
replies
79
views
Differential accessibility using DiffBinf
diffbind
1 day ago by
Shloka
• 0
0
votes
0
replies
85
views
vg call vs vg surject
vg
variation
graphs
updated 1 day ago by
GenoMax
141k • written 1 day ago by
aliraza3119
• 0
0
votes
1
reply
117
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Winter
• 0
2
votes
7
replies
1.2k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 1 day ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
190
views
Finding batch and outlayers
Pca
updated 1 day ago by
christopher medway
▴ 450 • written 1 day ago by
Tigran
• 0
2
votes
2
replies
181
views
PDB related issue
rcsb
pdb
updated 1 day ago by
noodle
▴ 580 • written 2 days ago by
Nafi
• 0
0
votes
0
replies
103
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
346
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 1 hour ago by
LauferVA
4.2k • written 2 days ago by
jinyu
▴ 10
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 1 day ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
434
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
2 days ago by
ashaneev07
▴ 20
0
votes
1
reply
151
views
Downloading full alignments from Pfam
pfam
updated 2 days ago by
GenoMax
141k • written 2 days ago by
bef1
• 0
0
votes
1
reply
738
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 2 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
3
votes
2
replies
271
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 1 day ago by
i.sudbery
19k • written 4 days ago by
vanbelj
▴ 40
0
votes
0
replies
109
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 1 day ago by
dariober
14k • written 2 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
268
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 2 days ago by
ATpoint
82k • written 3 days ago by
Francesco
▴ 10
0
votes
0
replies
129
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
3 days ago by
tnminh89
▴ 10
0
votes
0
replies
132
views
Filter low express genes in microarray data
microarray
3 days ago by
Chris
▴ 260
0
votes
1
reply
318
views
absolute path for symbolic links in Snakefile
Snakemake
updated 3 days ago by
Jesse
▴ 740 • written 11 days ago by
yifangt86
▴ 60
0
votes
2
replies
331
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 3 days ago by
Jesse
▴ 740 • written 5 days ago by
Broccoli
• 0
4
votes
3
replies
337
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 3 days ago by
Arup Ghosh
3.2k • written 4 days ago by
chaco001
▴ 40
1
vote
3
replies
361
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 2 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
O.rka
▴ 710
0
votes
2
replies
242
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
3 days ago by
Guille
• 0
4
votes
2
replies
274
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
1 day ago by
pairedttest
▴ 10
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 3 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
544
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
4 days ago by
biocellbio
• 0
4
votes
8
replies
609
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 3 days ago by
Alex Reynolds
35k • written 4 days ago by
J
▴ 10
4
votes
7
replies
660
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 3 days ago by
dsull
★ 5.9k • written 7 days ago by
qudrat.nii
▴ 10
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 4 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
3
votes
2
replies
319
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 4 days ago by
dsull
★ 5.9k • written 4 days ago by
Aaliya
▴ 10
3
votes
0
replies
193
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 4 days ago by
Ram
43k • written 4 days ago by
Claire Watson
▴ 60
0
votes
2
replies
270
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 4 days ago by
Ram
43k • written 4 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
197
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
4 days ago by
HarperReed
• 0
3
votes
3
replies
283
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 4 days ago by
GenoMax
141k • written 4 days ago by
sapuizait
▴ 10
1
vote
0
replies
154
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
4 days ago by
KABILAN
▴ 70
0
votes
0
replies
170
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 4 days ago by
Ram
43k • written 4 days ago by
SineWave
• 0
0
votes
0
replies
165
views
RNA-seq: full length gene
RNA-seq
updated 4 days ago by
Ram
43k • written 4 days ago by
Nargis
• 0
1
vote
7
replies
451
views
gvcf joint calling
WES
GATK
VCF
gVCF
2 days ago by
zihanss
• 0
0
votes
0
replies
152
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
4 days ago by
turcoa1
• 0
1,113 results • Page
2 of 23
Recent Votes
Answer: p-value in CIBERSORT
Answer: Can I have multiple active GDC download tokens?
Answer: Can I have multiple active GDC download tokens?
Comment: Can I have multiple active GDC download tokens?
Comment: Programmatically retrieving positions of protein active site residues
Comment: Programmatically retrieving positions of protein active site residues
Extracting genomic feature sequences from GTF/GFF files with AGAT
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Comment: Telescope issue
by
eleven11
• 0
Hello the output is A01940:33:GW2208142379th:3:1317:24126:3505 355 chr14 16651125 0 150M = 17034150 122900 GCTAACAGAGTTGAACCTTTCTATTG…
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
Looking at the [code here][1] `bundle_uuid` seems to be related to the submissions to HCA. Samples that ran on multiple lanes seem to have …
Comment: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
this is very true and increasingly true as time goes forward. thanks for supplementing this post with your own :-)
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
jeffrey.maurer.informatics
• 0
Thank you, but I've already checked out that site to see if I was missing anything and I don't see any answers to my questions there.
Answer: p-value in CIBERSORT
by
Aspire
▴ 320
You have not explicitly specified the number of permutations (which are used to calculate the p-value). The default value of the permutatio…
Comment: Telescope issue
by
GenoMax
141k
> CIGAR and query sequence are of different length [W::sam_read1] Parse error at line 9954941 Problem appears to be at that line. Can you …
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
▴ 320
- `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, …
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, …
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