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116,647 results • Page
1 of 2333
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
15
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
19 minutes ago by
DOBI
• 0
0
votes
0
replies
11
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
1 hour ago by
Ruqaiya
• 0
0
votes
0
replies
12
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
1 hour ago by
atharvakarkare14
▴ 10
0
votes
1
reply
51
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 1 hour ago by
atharvakarkare14
▴ 10 • written 3 hours ago by
WUSCHEL
▴ 750
4
votes
16
replies
478
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
1 hour ago by
Ruqaiya
• 0
0
votes
0
replies
18
views
What should I consider as FASTA for dataset?
PDB
FASTA
1 hour ago by
Nafi
• 0
30
votes
20
replies
1.2k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated just now by
i.sudbery
19k • written 1 day ago by
noodle
▴ 560
0
votes
0
replies
24
views
Differential accessibility using DiffBinf
diffbind
2 hours ago by
Shloka
• 0
0
votes
0
replies
34
views
vg call vs vg surject
variation
graphs
3 hours ago by
aliraza3119
• 0
0
votes
0
replies
31
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
3 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 7 hours ago by
Gordon Smyth
★ 7.0k • written 8 months ago by
Calum
▴ 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
0
replies
87
views
Finding batch and outlayers
Pca
updated 3 hours ago by
Ram
43k • written 8 hours ago by
Tigran
• 0
2
votes
2
replies
134
views
PDB related issue
rcsb
pdb
updated 8 hours ago by
noodle
▴ 560 • written 12 hours ago by
Nafi
• 0
0
votes
0
replies
63
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annoration
updated 3 hours ago by
Ram
43k • written 13 hours ago by
carlopecoraro2
★ 2.5k
0
votes
5
replies
199
views
What does it mean single base resolution in sequencing?
SNP
sequencing
58 minutes 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 3 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
383
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
14 hours ago by
ashaneev07
▴ 20
0
votes
1
reply
111
views
Downloading full alignments from Pfam
pfam
updated 16 hours ago by
GenoMax
141k • written 21 hours ago by
bef1
• 0
0
votes
1
reply
703
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 21 hours ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
1
vote
1
reply
196
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 10 hours ago by
ATpoint
82k • written 2 days ago by
vanbelj
▴ 40
0
votes
0
replies
74
views
adjusting for confounders in LMER in R
confounders
LMER
R
1 day ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
231
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 14 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
100
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
112
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
105
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
1
reply
292
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
302
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
291
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
324
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 12 hours ago by
Mensur Dlakic
★ 27k • written 2 days ago by
O.rka
▴ 710
0
votes
1
reply
193
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
226
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
193
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
469
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
574
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
627
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
290
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
180
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
252
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
184
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
2 days ago by
HarperReed
• 0
3
votes
3
replies
260
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sapuizait
▴ 10
1
vote
0
replies
143
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
160
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
153
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
419
views
gvcf joint calling
WES
GATK
VCF
gVCF
23 hours ago by
zihanss
• 0
0
votes
0
replies
145
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
3 days ago by
turcoa1
• 0
3
votes
3
replies
279
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
0
votes
0
replies
154
views
Designing single-stable RNA molecules
structure
RNA
3 days ago by
Edna
• 0
116,647 results • Page
1 of 2333
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Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
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
Comment: NGS forensics: how to know if data is fabricated
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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…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 560
Working on it - it's actually a bit difficult. Low coverage of ribosomal proteins. Low coverage of housekeeping genes ...I'm trying to find…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 560
I'm a bit against pubpeer - have you ever posted there? My gripe with them is that the posts are heavily moderated and EDITED to the point…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
Thanks Mensur! I'd add that in 9 out of 10 cases, you won't receive a reply to a request for raw data. That's just how scientists are, does…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
I had downloaded the two files in a similar manner actually.
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
ok, i'll try to use fastp. I have only used trimmomatic and cutadapt till now and they dont identify on its own. Except the graph in fastqc…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
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