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116,648 results • Page
1 of 2333
Sort: Rank
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Votes
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0
votes
1
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18
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
updated 23 minutes ago by
ATpoint
82k • written 40 minutes ago by
Lluís R.
★ 1.2k
0
votes
1
reply
35
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 1 hour ago by
i.sudbery
19k • written 1 hour ago by
DOBI
• 0
0
votes
0
replies
17
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
2 hours ago by
Ruqaiya
• 0
0
votes
0
replies
19
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
2 hours ago by
atharvakarkare14
▴ 10
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
60
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 2 hours ago by
atharvakarkare14
▴ 10 • written 4 hours ago by
WUSCHEL
▴ 750
5
votes
16
replies
496
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
2 hours ago by
Ruqaiya
• 0
0
votes
0
replies
27
views
What should I consider as FASTA for dataset?
PDB
FASTA
2 hours ago by
Nafi
• 0
33
votes
20
replies
1.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 1 hour ago by
i.sudbery
19k • written 1 day ago by
noodle
▴ 570
0
votes
0
replies
30
views
Differential accessibility using DiffBinf
diffbind
4 hours ago by
Shloka
• 0
0
votes
0
replies
36
views
vg call vs vg surject
variation
graphs
5 hours ago by
aliraza3119
• 0
0
votes
0
replies
35
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
5 hours 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 9 hours ago by
Gordon Smyth
★ 7.0k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
103
views
Finding batch and outlayers
Pca
updated 48 minutes ago by
christopher medway
▴ 450 • written 10 hours ago by
Tigran
• 0
2
votes
2
replies
136
views
PDB related issue
rcsb
pdb
updated 10 hours ago by
noodle
▴ 570 • written 13 hours ago by
Nafi
• 0
0
votes
0
replies
65
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
39 minutes ago by
carlopecoraro2
★ 2.5k
0
votes
5
replies
206
views
What does it mean single base resolution in sequencing?
SNP
sequencing
2 hours 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 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
388
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
15 hours ago by
ashaneev07
▴ 20
0
votes
1
reply
113
views
Downloading full alignments from Pfam
pfam
updated 18 hours ago by
GenoMax
141k • written 22 hours ago by
bef1
• 0
0
votes
1
reply
705
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 22 hours ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
2
votes
2
replies
211
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 1 hour ago by
i.sudbery
19k • written 2 days ago by
vanbelj
▴ 40
0
votes
0
replies
76
views
adjusting for confounders in LMER in R
confounders
LMER
R
1 day ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
232
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 16 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
101
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
1 day ago by
tnminh89
▴ 10
0
votes
0
replies
114
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
106
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
1
reply
293
views
absolute path for symbolic links in Snakefile
Snakemake
updated 1 day ago by
Jesse
▴ 740 • written 9 days ago by
yifangt86
▴ 60
0
votes
2
replies
303
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 1 day ago by
Jesse
▴ 740 • written 4 days ago by
Broccoli
• 0
2
votes
3
replies
293
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 1 day ago by
Arup Ghosh
3.2k • written 2 days ago by
chaco001
▴ 40
1
vote
3
replies
325
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 13 hours ago by
Mensur Dlakic
★ 27k • written 2 days ago by
O.rka
▴ 710
0
votes
1
reply
195
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 2 days ago by
Gordon Smyth
★ 7.0k • written 2 days ago by
hagl
▴ 10
0
votes
2
replies
227
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
1 day ago by
Guille
• 0
2
votes
1
reply
195
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 2 days ago by
Gordon Smyth
★ 7.0k • written 2 days ago by
pairedttest
▴ 10
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 2 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
475
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
2 days ago by
biocellbio
• 0
4
votes
8
replies
575
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 2 days ago by
Alex Reynolds
35k • written 3 days ago by
J
▴ 10
4
votes
7
replies
629
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 2 days ago by
dsull
★ 5.9k • written 6 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 2 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
2
replies
291
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 2 days ago by
dsull
★ 5.9k • written 3 days ago by
Aaliya
▴ 10
3
votes
0
replies
181
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 2 days ago by
Ram
43k • written 2 days ago by
Claire Watson
▴ 60
0
votes
2
replies
253
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 2 days ago by
Ram
43k • written 3 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
185
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
3 days ago by
HarperReed
• 0
3
votes
3
replies
262
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 2 days ago by
GenoMax
141k • written 3 days ago by
sapuizait
▴ 10
1
vote
0
replies
144
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
3 days ago by
KABILAN
▴ 50
0
votes
0
replies
161
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 2 days ago by
Ram
43k • written 3 days ago by
SineWave
• 0
0
votes
0
replies
155
views
RNA-seq: full length gene
RNA-seq
updated 2 days ago by
Ram
43k • written 3 days ago by
Nargis
• 0
1
vote
7
replies
421
views
gvcf joint calling
WES
GATK
VCF
gVCF
1 day ago by
zihanss
• 0
0
votes
0
replies
146
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
3 days ago by
turcoa1
• 0
3
votes
3
replies
280
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 3 days ago by
swbarnes2
14k • written 3 days ago by
M
• 0
116,648 results • Page
1 of 2333
Recent Votes
Answer: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
NGS forensics: how to know if data is fabricated
Answer: ChIP-seq datasets: input samples omitted?
Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
ATpoint
82k
Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I followed your advice and it seems that I'm getting results comparable to what I was getting before. Upon checking with `wc -l` on the ori…
Comment: Finding batch and outlayers
by
christopher medway
▴ 450
You could perform an ANOVA to test if there is a significant association between batch number and a given Principal Component
Comment: ChIP-seq datasets: input samples omitted?
by
i.sudbery
19k
Fascinating! We also use inputs when doing metagene to protect against those situations where regions up or downstream of our metagene al…
Answer: How to solve DESeq2 Error in checkFullRank(modelMatrix)?
by
i.sudbery
19k
See the section on non full rank design matrices in the DESeq2 manual. In this case your problem is that healthy and 0dpi samples are e…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
Can you clarify what you mean by "100% of reads pass cutadapt, even though 70% of reads contain adapters and get trimmed. " did you set a m…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
I don't follow your argument for distinguishing between genomic contamination and freud. A data set being bad in terms of genomic contamin…
Comment: What does it mean single base resolution in sequencing?
by
jinyu
▴ 10
Thank you for your detail and great explanation. I do need more time to understand these. And there is still something compuzzling me. For …
Answer: Is it possible to bulk download files from GEO repository?
by
atharvakarkare14
▴ 10
Try using this library [GEOparse][1] [1]: https://github.com/guma44/GEOparse
Answer: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
OK. Problem solved. The problem was from my end. Thank you both for helping !!
Comment: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
Appreciate the suggestion, but that ship has sailed and reached the other shore. This happened 10+ years ago. To the best of my knowledge n…
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
Files are not opening in any of the computer (ubuntu/windows). I rereun snpEff annotation but still output html files are having missing im…
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
I reinstalled nodejs: > sudo apt-get install nodejs Its already up to date with version v10.19.0
Answer: NGS forensics: how to know if data is fabricated
by
Prash
▴ 280
Mensur, if I were you, I'd probably contact the CA directly and check with him whether they have reproduced the works recently. There coul…
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