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116,732 results • Page
3 of 2335
Sort: Rank
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1
vote
1
reply
135
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Ruqaiya
• 0
0
votes
1
reply
272
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 3 days ago by
trausch
★ 1.9k • written 20 days ago by
zec018
• 0
0
votes
0
replies
101
views
LEfSe
LEfSe
3 days ago by
benkosta
• 0
0
votes
0
replies
88
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
3 days ago by
Sara
▴ 30
1
vote
4
replies
387
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
3 days ago by
hagl
▴ 10
0
votes
5
replies
256
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 2 hours ago by
Mohamed Abderrahmane
▴ 20 • written 4 days ago by
matteo.levorato
• 0
0
votes
2
replies
151
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
4 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
142
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 4 days ago by
i.sudbery
19k • written 4 days ago by
DOBI
• 0
0
votes
0
replies
97
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
4 days ago by
atharvakarkare14
▴ 30
7
votes
16
replies
698
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
4 days ago by
Ruqaiya
• 0
0
votes
2
replies
197
views
What should I consider as FASTA for dataset?
PDB
FASTA
3 days ago by
Nafi
• 0
38
votes
24
replies
1.9k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 3 days ago by
i.sudbery
19k • written 5 days ago by
noodle
▴ 580
0
votes
0
replies
108
views
Differential accessibility using DiffBinf
diffbind
4 days ago by
Shloka
• 0
0
votes
0
replies
93
views
vg call vs vg surject
vg
variation
graphs
updated 3 days ago by
GenoMax
142k • written 4 days ago by
aliraza3119
• 0
0
votes
1
reply
132
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Winter
• 0
2
votes
7
replies
1.3k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 4 days ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
206
views
Finding batch and outlayers
Pca
updated 4 days ago by
christopher medway
▴ 450 • written 4 days ago by
Tigran
• 0
2
votes
2
replies
194
views
PDB related issue
rcsb
pdb
updated 4 days ago by
noodle
▴ 580 • written 4 days ago by
Nafi
• 0
0
votes
0
replies
109
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
4 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
426
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 2 days ago by
LauferVA
4.2k • written 4 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 4 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
452
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
4 days ago by
ashaneev07
▴ 20
0
votes
1
reply
168
views
Downloading full alignments from Pfam
pfam
updated 4 days ago by
GenoMax
142k • written 4 days ago by
bef1
• 0
0
votes
1
reply
747
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 4 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
3
votes
2
replies
290
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 4 days ago by
i.sudbery
19k • written 6 days ago by
vanbelj
▴ 40
0
votes
0
replies
120
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 3 days ago by
dariober
14k • written 5 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
296
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Francesco
▴ 10
0
votes
0
replies
137
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
5 days ago by
tnminh89
▴ 10
0
votes
0
replies
141
views
Filter low express genes in microarray data
microarray
5 days ago by
Chris
▴ 260
0
votes
1
reply
330
views
absolute path for symbolic links in Snakefile
Snakemake
updated 5 days ago by
Jesse
▴ 740 • written 13 days ago by
yifangt86
▴ 60
0
votes
2
replies
341
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 5 days ago by
Jesse
▴ 740 • written 8 days ago by
Broccoli
• 0
4
votes
3
replies
360
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 5 days ago by
Arup Ghosh
3.2k • written 6 days ago by
chaco001
▴ 40
1
vote
3
replies
382
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 4 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
O.rka
▴ 710
0
votes
2
replies
253
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
6 days ago by
Guille
• 0
4
votes
2
replies
298
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
3 days ago by
pairedttest
▴ 10
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 6 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
565
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
6 days ago by
biocellbio
• 0
4
votes
8
replies
647
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 6 days ago by
Alex Reynolds
35k • written 7 days ago by
J
▴ 10
4
votes
7
replies
685
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 6 days ago by
dsull
★ 5.9k • written 10 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 6 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
3
votes
2
replies
330
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 6 days ago by
dsull
★ 5.9k • written 7 days ago by
Aaliya
▴ 10
3
votes
0
replies
207
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 6 days ago by
Ram
43k • written 7 days ago by
Claire Watson
▴ 60
0
votes
2
replies
281
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 6 days ago by
Ram
43k • written 7 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
204
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
7 days ago by
HarperReed
• 0
3
votes
3
replies
303
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 6 days ago by
GenoMax
142k • written 7 days ago by
sapuizait
▴ 10
1
vote
0
replies
158
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
7 days ago by
KABILAN
▴ 70
0
votes
0
replies
176
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 6 days ago by
Ram
43k • written 7 days ago by
SineWave
• 0
0
votes
0
replies
172
views
RNA-seq: full length gene
RNA-seq
updated 6 days ago by
Ram
43k • written 7 days ago by
Nargis
• 0
1
vote
7
replies
490
views
gvcf joint calling
WES
GATK
VCF
gVCF
5 days ago by
zihanss
• 0
0
votes
0
replies
154
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
7 days ago by
turcoa1
• 0
116,732 results • Page
3 of 2335
Recent Votes
C: Split Fastq Files Into Chunks Of 1M Reads
Answer: How many reads for WGS Sequencing?
Answer: How many reads for WGS Sequencing?
Comment: How to Calulate Allele Frequency from a VCF File?
Answer: Introduce SNPs on FASTA
Answer: how to split multi-fasta file into single fasta file named by header
How to Calulate Allele Frequency from a VCF File?
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Recent Replies
Comment: How does gene length effect the number of reads mapped
by
i.sudbery
19k
The number of reads for a gene is almost exactly linearly proportional to the length of the gene. In paired-end sequencing, we generally co…
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
Answer: DSEQ2 analysis
by
ATpoint
82k
The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
Comment: Generating mpileup file using samtools
by
Joe
21k
It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This is great also for multiline fastas
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This only works for the first line of sequences.
Answer: What purposes can TPM values be used for?
by
b.contreras.moreira
▴ 180
In case it helps: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
alifafiq1
• 0
Thank you @AT point. I was planning to use DESeq2 and use the alternate hypothesis (lessAbs) too considering that is the only package that …
Comment: Does comparing two different groups to a common third group introduce bias in th
by
ATpoint
82k
Note that by basic algebra A vs C and B vs C is the same as A vs B, so you might rethink your analysis to answer your question in a much si…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
Yes, why not? If it works for you like that, bingo!
Answer: Does comparing two different groups to a common third group introduce bias in th
by
christopher medway
▴ 450
You are testing groups A and B to a common baseline (C) - I don't see that there is anything wrong with doing that. It is a fairly common a…
Comment: HOMER on AWS
by
clairechung112
• 0
Hi. I guess it is solved by now, but as I did not find the answer immediately online, here is the answer I posted on a relevant question: h…
Answer: homer not configured properly
by
clairechung112
• 0
A late reply, but I just solved exactly the same error upon a request in the team. Please see if it helps in case anyone meets the same err…
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