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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
5
replies
323
views
Best way to deal with overlapping read names in merged BAM files
picard
MarkDuplicates
3 days ago by
shpak.max
▴ 50
0
votes
1
reply
188
views
merging Seurat objects after SCT
Seurat
SCT
updated 3 days ago by
Ram
43k • written 3 days ago by
michelle.swarovski
• 0
0
votes
1
reply
167
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 3 days ago by
GenoMax
141k • written 3 days ago by
haiying.kong
▴ 360
0
votes
2
replies
238
views
RNAseq 1 control 2 different treatment
RNA-seq
3 days ago by
matteo.levorato
• 0
1
vote
0
replies
129
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 3 days ago by
Ram
43k • written 3 days ago by
Oscar
▴ 10
1
vote
2
replies
195
views
CombineGVCFs vs. MergeVcfs
CombineGVCFs
MergeVcfs
GATK
WGS
GVCF
updated 2 days ago by
Jeremy Leipzig
22k • written 3 days ago by
Sd
• 0
0
votes
0
replies
125
views
News:
Deadline Approaching: PETs for Public Health Challenge
privacy
public-health-challenge
updated 3 days ago by
Ram
43k • written 3 days ago by
polarise
▴ 380
0
votes
0
replies
132
views
How should I make kallisto indexes?
kallisto
updated 3 days ago by
GenoMax
141k • written 3 days ago by
bioinfo
▴ 150
1
vote
2
replies
186
views
Problem with Sniffles pipeline and SV calling help
SV
sniffles
StructuralVariant
updated 3 days ago by
GenoMax
141k • written 3 days ago by
njornet
▴ 20
4
votes
0
replies
162
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
3 days ago by
Biostar
2.6k
2
votes
1
reply
213
views
Trouble understanding seemingly contradicting results of GSE analysis (contradicting enriched GO terms with similar negative NES scores)
GSEA
pathways
GO-terms
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Manko47
• 0
4
votes
6
replies
389
views
Odd results with BLAST remote
blast
remote
NCBI
updated 3 days ago by
b.contreras.moreira
▴ 160 • written 4 days ago by
Begonia_pavonina
▴ 150
6
votes
8
replies
466
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 2 days ago by
dariober
14k • written 4 days ago by
manaswiniparija3
▴ 40
2
votes
0
replies
189
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
4 days ago by
Alexander
▴ 220
1
vote
1
reply
158
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 3 days ago by
GenoMax
141k • written 4 days ago by
eesiribloom
▴ 80
0
votes
0
replies
124
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
4 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
126
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
4 days ago by
adarsh_pp
▴ 40
2
votes
4
replies
332
views
Which command ro run MAKER pipeline for gene annotation ?
run.
command
to
MAKERpipeline.
updated 4 days ago by
GenoMax
141k • written 4 days ago by
Sony
▴ 10
0
votes
0
replies
134
views
FreeBayes detection capacity
reads
freebayes
long
4 days ago by
quentinperriere
• 0
0
votes
2
replies
211
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
2 days ago by
DKA
▴ 40
0
votes
2
replies
233
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
3 days ago by
rj.rezwan
• 0
7
votes
7
replies
833
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 3 days ago by
Dunois
★ 2.5k • written 4 days ago by
AdviceSeeker
• 0
0
votes
0
replies
154
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
4 days ago by
Hien
• 0
0
votes
2
replies
261
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
2 days ago by
Koketso
• 0
1
vote
3
replies
391
views
Extracting data from a local NCBI taxonomy database
R
NCBI
xml
E-utilities
Blast
updated 5 days ago by
josev.die
▴ 60 • written 17 days ago by
Begonia_pavonina
▴ 150
0
votes
0
replies
180
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 4 days ago by
Ram
43k • written 5 days ago by
menyawino
• 0
0
votes
0
replies
154
views
News:
Online course: Network Analysis in R
NetworkAnalyis
R
5 days ago by
carlopecoraro2
★ 2.5k
1
vote
3
replies
310
views
Ensembl gene id conversion
biomart
ensembl
updated 3 days ago by
ATpoint
81k • written 5 days ago by
naveedhasan2000
• 0
1
vote
2
replies
290
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 3 days ago by
Istvan Albert
100k • written 5 days ago by
Jiang
• 0
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 1 day ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
2
votes
3
replies
342
views
Deseq2 : Paired analysis or otherwise
linear-regression
paired-analysis
DESeq2
longitudinal-analysis
updated 3 days ago by
ATpoint
81k • written 5 days ago by
IM
• 0
2
votes
1
reply
278
views
How to highlight genes on genome visual reprezentation/what tool to use?
gene
genome
updated 5 days ago by
Alex Reynolds
35k • written 5 days ago by
natami
▴ 10
1
vote
1
reply
477
views
adding gene and CDS feature types in ensemble gtf annotation with transcript and exon features
GTF
GFF
transcript
CDS
exon
updated 5 days ago by
Pratik
★ 1.0k • written 5 days ago by
memy
▴ 20
0
votes
0
replies
195
views
Different flagstat number after using MergeBamAlignment
MergeBamAlignment
samtools
flagstat
5 days ago by
ThomasLam
• 0
3
votes
4
replies
350
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI.
cDNA
updated 5 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
Sony
▴ 10
0
votes
0
replies
173
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
6 days ago by
YiweiZhu
▴ 30
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 6 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
0
votes
0
replies
179
views
Somatic and Germline variant calling for tumor, normal and blood sample
germline
variants
somatic
updated 5 days ago by
Ram
43k • written 6 days ago by
anitharavichandran2211
• 0
2
votes
2
replies
260
views
Ciriquant not configuring hisat2 indexed files
ciriquant
2 hours ago by
Atul K.
• 0
1
vote
1
reply
245
views
How to handle more than 1 SRA Run per Experiment?
SRA
Preprocessing
updated 6 days ago by
ATpoint
81k • written 6 days ago by
Janmajay
• 0
0
votes
2
replies
299
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
5 days ago by
O.rka
▴ 710
0
votes
6
replies
513
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
3 days ago by
Dunois
★ 2.5k
1
vote
1
reply
261
views
How do I identify gene duplication or paralogs in an annotated reference genome assembly
blast
duplication
paralog
genome
updated 6 days ago by
sansan_96
▴ 80 • written 6 days ago by
brimaloney24
• 0
4
votes
7
replies
525
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 5 days ago by
Ram
43k • written 6 days ago by
AHerik
▴ 20
0
votes
0
replies
172
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 6 days ago by
GenoMax
141k • written 6 days ago by
zec018
• 0
5
votes
5
replies
835
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq
Blacklist
updated 6 days ago by
Ram
43k • written 10 months ago by
Emily Wasson
▴ 30
0
votes
0
replies
187
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 6 days ago by
Ram
43k • written 6 days ago by
roussine
▴ 10
0
votes
0
replies
170
views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
ATAC-seq
HOMER
6 days ago by
Ronin
• 0
4
votes
4
replies
367
views
How do I install plink2 on a mac?
plink2
plink
updated 4 days ago by
zx8754
11k • written 6 days ago by
emilija.romic
▴ 10
0
votes
5
replies
459
views
Is it possible to set different tracks to the same scale in JBrowse
track
jbrowse
updated 6 days ago by
Ram
43k • written 8 days ago by
Jose
• 0
1,000 results • Page
3 of 20
Recent Votes
Answer: Plink merge errors.
Gene Set Enrichment Analysis
Gene Set Enrichment Analysis
A: Counting Number Of Bases In A Fastq File
Free/open source 23andme-like analysis
Comment: Free/open source 23andme-like analysis
Answer: Missing protein (VEGF-A) in String db
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54k
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Recent Replies
Answer: Plink merge errors.
by
Dinmukhamed
• 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
Pierre Lindenbaum
161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
b.contreras.moreira
▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
Comment: Korean human genome reference file
by
SeoGyun
• 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 510
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
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