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121,625 results • Page
1 of 2433
Sort: Rank
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Votes
Replies
10
votes
14
replies
60k
views
11 follow
Tools to view fastq file
fastq
updated 20 minutes ago by
GenoMax
152k • written 9.2 years ago by
Roden Luo
▴ 40
1
vote
2
replies
225
views
how extract CpG methylatiuon calls from nanopore long sequencing bam file ?
methylation
updated 3 hours ago by
Istvan Albert
102k • written 4 days ago by
reziyamaimaiti0331
• 0
0
votes
0
replies
47
views
News:
Online Course: Phylogenomics – 1–5 December
Phylogenomics
DivergenceTimeEstimation
PhylogeneticInference
7 hours ago by
Physalia-courses
★ 2.6k
3
votes
3
replies
239
views
How do I generate synthetic 16S RNA gene sequences?
16S
sequence
rRNA
Infernal
augmentation
data
oversampling
cmemit
updated 7 hours ago by
shelkmike
★ 1.7k • written 3 days ago by
Max Sikolenko
▴ 70
0
votes
1
reply
125
views
Minimap2 Output
with
Singletons
Interleaved
Minimap2
updated 10 hours ago by
Istvan Albert
102k • written 2 days ago by
Jon
• 0
843
votes
170
replies
183k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
3.6k • written 8.6 years ago by
Istvan Albert
102k
0
votes
1
reply
93
views
Liftover from mm10 to CAST/PWK – Very Low Mapping Rate & Missing Chain File
Liftover
updated 10 hours ago by
GenoMax
152k • written 1 day ago by
daffodil
▴ 10
8
votes
9
replies
552
views
Does edgeR supports random effects?
RNASeq
voom
randomeffects
edgeR
limma
updated 10 minutes ago by
Gordon Smyth
★ 8.2k • written 4 days ago by
406339165
▴ 10
1
vote
3
replies
171
views
Intro + Question
Internship
Contribution
updated 10 hours ago by
Pierre Lindenbaum
166k • written 1 day ago by
akshitabadrinath
• 0
2
votes
1
reply
126
views
News:
Feedback needed on new user-friendly BED file tool
bedtools
bed
updated 2 days ago by
GenoMax
152k • written 2 days ago by
nadia
• 0
2
votes
3
replies
219
views
New to Bioinformatics, Phage genome investigation
prostT5
genetics
phages
bacteriophage
sphae
updated 2 days ago by
Michael
56k • written 2 days ago by
Hanhan2000
▴ 10
1
vote
2
replies
176
views
Issues for Purchasing The Biostar Handbook – Professional Edition
Biostar
handbook
1 day ago by
Srijan
• 0
0
votes
3
replies
200
views
STAR alignment to small fasta file failing
seq
STAR
alignment
RNA
updated 4 hours ago by
GenoMax
152k • written 3 days ago by
Annie
• 0
1
vote
4
replies
290
views
STAR aligned BAM files
genome_aligned
STAR
BAM
files
transcripts
updated 3 days ago by
Ram
45k • written 3 days ago by
rajdeepboral00
▴ 70
0
votes
0
replies
257
views
Statistical comparison of chr8 amplifications in matched primary vs metastatic WGS samples using log2 CN data
statistics
copy-number
cnvkit
updated 3 days ago by
Ram
45k • written 3 days ago by
Dalal
• 0
1
vote
1
reply
163
views
undefined chro name in vcf header
UnplacedContigs
Header
vcf
RandomContigs
3 days ago by
Mahdi&Christ
▴ 20
3
votes
1
reply
164
views
Fixing MGI Sequence Headers - FASTQ Format
fastq
mgi
updated 3 days ago by
GenoMax
152k • written 3 days ago by
joe_genome
▴ 70
0
votes
1
reply
152
views
how extract CpG methylatiuon calls from nanopore long sequencing bam file ?
methylation
updated 1 day ago by
Ram
45k • written 3 days ago by
reziyamaimaiti0331
• 0
2
votes
4
replies
1.8k
views
Draw a genome map with CGView server?
assembly
genome map
CGView
updated 9 hours ago by
Max Sikolenko
▴ 70 • written 6.2 years ago by
El Niño
▴ 10
0
votes
1
reply
614
views
The branch point is not labelled as expected
monocle
updated 3 days ago by
wschen97
• 0 • written 23 months ago by
Lin
• 0
10
votes
11
replies
14k
views
8 follow
Significance of the term "tile" in sequencing?
genomics
updated 5 hours ago by
Christopher
▴ 10 • written 4.4 years ago by
joe_genome
▴ 70
0
votes
2
replies
240
views
chromosome ideogram
chromosome
updated 3 days ago by
cmdcolin
★ 4.3k • written 4 days ago by
zhangmyharper
• 0
1
vote
2
replies
258
views
bin reassembly question
data
metawrap
assembly
shotgun
updated 3 days ago by
Mensur Dlakic
★ 29k • written 4 days ago by
shevch2009
▴ 20
3
votes
5
replies
322
views
What is the best way to handle "?" in the 7th column (strand) of GTF files?
fasta
STAR
ENSEMBL
GTF
RefSeq
updated 4 days ago by
GenoMax
152k • written 4 days ago by
ki
• 0
0
votes
0
replies
131
views
News:
Workshop: Virtual RNA-seq Analysis, July 29–31
RNASeq
workshop
UConn
4 days ago by
zsc25001
▴ 10
0
votes
0
replies
236
views
Problems integrating DEXSeq2 + stageR + DRIMSeq + DESeq2 for transcript group/promoter usage analysis
differential-transcript-usage
differential-gene-expression
dexseq
deseq2
drimseq
4 days ago by
LuciaNhu
▴ 10
0
votes
1
reply
248
views
lifting over mitochondrial SNPs between reference genomes
bcftools
liftover
hg19
picard
VCF
updated 4 days ago by
benformatics
4.1k • written 5 days ago by
112233
• 0
0
votes
3
replies
281
views
Merging segment CNV files
CNV
updated 1 day ago by
Ram
45k • written 5 days ago by
avelarbio46
▴ 30
0
votes
1
reply
4.7k
views
convert PLINK file to genepop
SNP
genome
snp
updated 5 days ago by
Noeliton
• 0 • written 8.4 years ago by
age00
• 0
7
votes
6
replies
538
views
6 follow
How do I interpert PCA before differential expression analysis
EDA
DESeq2
PCA
QC
updated 4 days ago by
Mensur Dlakic
★ 29k • written 5 days ago by
gogeni5529
▴ 80
3
votes
6
replies
462
views
RRBS (Reduced Representation Bisulfite Sequencing)
Trim
RRBS
Galore
updated 3 days ago by
dthorbur
★ 3.0k • written 5 days ago by
sk_24
• 0
0
votes
0
replies
166
views
News:
Course - Population Genomics Using Ancient DNA Data - Online, September 22-26
PopulationGenomics
aDNA
5 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
293
views
Repeat expansion VCF from ONT RU field and displayRU differences with gnomAD STR dataset repeat units
VCF
STRs
annotation
5 days ago by
ieie
▴ 20
39
votes
11
replies
6.2k
views
12 follow
What Are Your Most-Used Public Data Repositories?
database
updated 5 days ago by
ATpoint
88k • written 11.9 years ago by
Sean Davis
27k
5
votes
6
replies
2.3k
views
7 follow
Is there a database of bioinformatics tools & databases?
ebi
entrez
updated 5 days ago by
ehaag
▴ 90 • written 3.6 years ago by
LauferVA
4.8k
3
votes
9
replies
2.7k
views
how can I search for a new release data?
next-gen
microarray
RNA-Seq
homology-modelling
updated 5 days ago by
ehaag
▴ 90 • written 10.4 years ago by
yoingchinchina
▴ 20
0
votes
3
replies
472
views
How to trace back found motifs from homer and fimo to bed file so that visualization in genome browser
motif
updated 5 days ago by
GenoMax
152k • written 5 days ago by
EdisonJ
• 0
0
votes
0
replies
198
views
Problem at running Automlsa2
tree
phylogenetic
outgroup
selection
updated 6 days ago by
GenoMax
152k • written 6 days ago by
muhammadirfanulislambcsir
• 0
0
votes
0
replies
192
views
Comparative value conversions between fold enrichment-SHINYGO and Stringdb Score
stringdb
shinygo
6 days ago by
feliyon86
• 0
0
votes
1
reply
241
views
Output of heatmap2 tool on Galaxy
heatmap2
updated 6 days ago by
GenoMax
152k • written 6 days ago by
Stefano
• 0
1
vote
3
replies
327
views
Download data from BV-BRC
bv-brc
arm
download
bvbrc
gene
updated 6 days ago by
GenoMax
152k • written 6 days ago by
rica01
• 0
2
votes
3
replies
520
views
Splitting chromosomes into contigs within BAM and GTF files
samtools
gtf
chromosome
annotation
bam
updated 6 days ago by
rfran010
★ 1.6k • written 11 days ago by
MAB
▴ 10
0
votes
3
replies
351
views
concoct in metawrap binning module - use all available threads instead of requested
binning
concoct
metawrap
module
5 days ago by
shevch2009
▴ 20
3
votes
17
replies
1.0k
views
Inverted TSS Enrichment Plot
ATACSeq
deeptools
3 days ago by
nmalexan
• 0
5
votes
1
reply
287
views
hg38 vs GRCh38 chr prefix
human
genome
reference
updated 6 days ago by
GenoMax
152k • written 6 days ago by
DBScan
▴ 510
2
votes
4
replies
1.7k
views
Problem using FastML for ancestral sequence reconstruction
FastML
ancestral-sequence-reconstruction
fastml.std
updated 6 days ago by
christian.baumann
▴ 10 • written 3.1 years ago by
CM
• 0
2
votes
1
reply
284
views
Too many contigs in Spades output
spades
Assembly
updated 6 days ago by
GenoMax
152k • written 6 days ago by
waqaskhokhar999
▴ 160
1
vote
3
replies
388
views
How to handle contamination in 16s amplicon data
16s
amplicon
updated 6 days ago by
GenoMax
152k • written 6 days ago by
1769mkc
★ 1.3k
3
votes
12
replies
967
views
Strandedness issues in STAR quantification
STAR
stranded
updated 6 days ago by
GenoMax
152k • written 11 days ago by
marek.gierlinski
▴ 20
7
votes
7
replies
635
views
RNA-seq low quality sample in downstream analysis
Mitochondrial
genes
RNA-seq
DESeq2
updated 4 days ago by
Aleksandra
▴ 30 • written 6 days ago by
Yingying
▴ 50
121,625 results • Page
1 of 2433
Recent Votes
Answer: How do I generate synthetic 16S RNA gene sequences?
Answer: Does edgeR supports random effects?
Answer: Tools for bulk RNA-seq celltype deconvolution
How do I generate synthetic 16S RNA gene sequences?
Comment: Intro + Question
Comment: Draw a genome map with CGView server?
A: single cell RNA seq Differential Expression using MAST
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AlienPumpkinPie
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daffodil
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Recent Replies
Comment: Tools to view fastq file
by
GenoMax
152k
`FinchTV` is meant for use with ABI chromatogram (sanger sequencing) files. Don't think it can read fastq files. In any case there is no ca…
Comment: Does edgeR supports random effects?
by
Gordon Smyth
★ 8.2k
Subsetting to half the data will obviously change the results. The mean-variance relationship and the inter-block correlation need to be re…
Answer: Tools to view fastq file
by
chuckles
• 0
Obviously a very late response, here, but for anyone looking for answers now or in future: I'm sure there are other tools, but the one I…
Answer: how extract CpG methylatiuon calls from nanopore long sequencing bam file ?
by
Istvan Albert
102k
The BAM file has tags that contain the information you need. There are tags such as: * `MM`: Modified base motif and positions. …
Comment: Does edgeR supports random effects?
by
406339165
▴ 10
**The code was super helpful — thank you so much, Gordon! (cc: @gordonsmyth)** I ran the code and got the following results, but I’m a bit…
Comment: STAR alignment to small fasta file failing
by
GenoMax
152k
I suggest that you give another (bbmap, bwa-mem2, bowtie etc) NGS aligner a try. STAR is splice-aware and likely has default options that l…
Comment: Significance of the term "tile" in sequencing?
by
Ram
45k
Open a new question, add the detail you just gave GenoMax in that question, then delete this answer.
Comment: Significance of the term "tile" in sequencing?
by
Christopher
▴ 10
It's from NovaSeq6000
Comment: Significance of the term "tile" in sequencing?
by
Christopher
▴ 10
Okay, I apologize. Since I saw that this issue had already been mentioned in the forum, I thought it wasn’t necessary to create a new topic…
Answer: How do I generate synthetic 16S RNA gene sequences?
by
shelkmike
★ 1.7k
Maybe, the following is worth doing:<br> 1) First, you need to understand how much the natural sequences differ from the covariance model. …
Comment: STAR alignment to small fasta file failing
by
Annie
• 0
There are 8 reference sequences in the fasta, total about 9,000 bases. I'm using STAR because it's what I've been using for these data and …
Comment: How do I generate synthetic 16S RNA gene sequences?
by
Max Sikolenko
▴ 70
> Why do you need to augment 16S rRNA sequences, given that tens of millions are already available? If your main reason is sequence diversi…
Comment: Draw a genome map with CGView server?
by
Max Sikolenko
▴ 70
Circular genome maps of unassembled contigs do not make much sense, unfortunately. Anyway, > Which tools should I use for drawing bacteria…
Answer: Minimap2 Output
by
Istvan Albert
102k
Minimap 2 has two outputs the PAF format and the SAM format. Each has a documentation that describes how the information is encoded. In …
Comment: Intro + Question
by
Pierre Lindenbaum
166k
how about just asking this kind of questions in their github repo ?
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