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121,125 results • Page
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Efficiently find regions in bed file that are within start and end regions of another bed file.
bedtools
intersect
ranges
genomic
updated just now by
Pierre Lindenbaum
166k • written 4 hours ago by
rxs1018
• 0
0
votes
0
replies
50
views
Alternative to PASApipeline
transcriptomics
annotation
6 hours ago by
lagartija
▴ 160
0
votes
1
reply
63
views
16S Libraries With Non-Purified Short Fragments
Sequencing
16S
Libraries
Magnetic
Beads
updated 5 hours ago by
GenoMax
151k • written 6 hours ago by
alenew.am
▴ 10
837
votes
170
replies
175k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
1
reply
70
views
How to map polyA tails to barcodes in paired end reads for single cell RNA-seq
RNA-seq
cell
polyA
single
updated 5 hours ago by
GenoMax
151k • written 6 hours ago by
Ana
▴ 10
7
votes
6
replies
4.8k
views
Questions related to ChromHMM+using MACS2 peak calling output bed file as input for ChromHMM?
macs2
ChIP-Seq
ChromHMM
MACS2
CHROMHMM
updated 7 hours ago by
luminea
▴ 10 • written 5.9 years ago by
m.sadman.sakib
▴ 120
4
votes
5
replies
330
views
Editing and Adding to a GTF file
Annotation
Gene
GTF
ID
updated 8 hours ago by
gernophil
▴ 120 • written 1 day ago by
Keem Uarren Eiryll
▴ 10
3
votes
2
replies
98
views
Averaging multiple IgG BAM files for use as a control in ChromHMM
ChromHMM
bam
averag
updated 7 hours ago by
ATpoint
88k • written 8 hours ago by
luminea
▴ 10
3
votes
3
replies
330
views
Deduplication rate of shotgun metagenomes using fastqc
metagenome
fastqc
shotgun
deduplication
updated 8 hours ago by
colindaven
7.4k • written 5 days ago by
vikasmh111
• 0
0
votes
2
replies
109
views
differential exon usage from Salmon outputs
edgeR
diffSpliceDGE
DEU
salmon
7 hours ago by
n_navy
• 0
0
votes
0
replies
59
views
News:
online course: Introduction to Genome Annotation
Gene-Prediction
Genome-Annotation
Gene-Models
11 hours ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
243
views
ValueError: Found array with 0 sample(s) (shape=(0, 138)) while a minimum of 1 is required. In metawrap - concoct binning module
concoct
metawrap
module
8 hours ago by
shevch2009
• 0
0
votes
3
replies
167
views
Circular heatmap using circos.heatmap in R
R
circos
heatmap
circularheatmap
updated 6 hours ago by
GenoMax
151k • written 15 hours ago by
Yukta
• 0
0
votes
0
replies
86
views
Zebrafish phenotype ontology enrichment analyses
ontology
zebrafish
22 hours ago by
Li
• 0
0
votes
2
replies
140
views
Sequence Duplication for Single-End 3RAD Data
duplication
reduced-representation
40 minutes ago by
Sarah
• 0
0
votes
0
replies
85
views
Cytoscape KEGG plots reverting to original layout after changing style or column
kegg
cytoscape
1 day ago by
Adrian
• 0
1
vote
6
replies
1.0k
views
6 follow
Not retrieving Mitochondrial Genes in Single Cell analysis
single-cell
updated 22 hours ago by
Ram
45k • written 10 months ago by
guioliveirareis
▴ 10
0
votes
0
replies
94
views
News:
Ancient Metagenomics course - online, May 27-29
ancient-metagenomics
aDNA
aMeta
1 day ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
129
views
Issues running scAPAtrap
scAPAtrap
polyA
scRNAseq
updated 1 day ago by
GenoMax
151k • written 1 day ago by
Ana
▴ 10
5
votes
3
replies
236
views
What are BED files?
BED
updated 20 hours ago by
Alex Reynolds
36k • written 1 day ago by
Besoa
• 0
3
votes
8
replies
407
views
ggplot make boxplots more wide
ggplot2
r
1 day ago by
Nona
▴ 90
2
votes
1
reply
180
views
Minimum number of samples for multi-omics data integration
multi-omics
updated 1 day ago by
Ram
45k • written 1 day ago by
Tundup
▴ 10
1
vote
0
replies
129
views
News:
Workshop: Virtual Genome Annotation, May 27–29
GenomeAnnotation
workshop
UConn
1 day ago by
zsc25001
▴ 10
1
vote
1
reply
169
views
Assigning a string variable on Visual Studio using python
python
visual-studio
updated 1 day ago by
Ram
45k • written 2 days ago by
arthur_alexander83
• 0
4
votes
4
replies
288
views
Tool:
Gene Exons Painter
Genomics
Visualisation
Exons
Transcripts
Isoforms
updated 1 day ago by
benformatics
4.1k • written 2 days ago by
Rafal
▴ 70
0
votes
0
replies
127
views
News:
Course online:Functional programming in R, May 27-30
R
programming
functional
2 days ago by
soledad.esteban
• 0
3
votes
1
reply
205
views
Herald:
The Biostar Herald for Monday, May 05, 2025
herald
updated 2 days ago by
cmdcolin
★ 4.2k • written 2 days ago by
Biostar
3.5k
0
votes
0
replies
110
views
How to generate .AED files from .CEL files using Linux (Affymetrix CytoScan HT-CMA 96F)
HT-CMA-96
analysis
data
affymetrix
microarray
2 days ago by
genetixs
▴ 20
0
votes
0
replies
123
views
News:
Online course - Introduction to GWAS
R
GWAS
Statistics
2 days ago by
Physalia-courses
★ 2.6k
4
votes
3
replies
248
views
Sample level genotype mapping in plink vcf output
VCF
updated 1 day ago by
Pierre Lindenbaum
166k • written 2 days ago by
1769mkc
★ 1.3k
6
votes
2
replies
274
views
Tool:
RNAseq Power Calculator
calculator
Replicates
RNAseq
Statistics
Power
2 days ago by
Rafal
▴ 70
1
vote
1
reply
215
views
Association (Protein interaction) in Intact database results what can really mean?
protein-protein-interaction
database
protein
proteins
Intact
updated 2 days ago by
Mensur Dlakic
★ 29k • written 3 days ago by
Bendegúz
• 0
1
vote
4
replies
387
views
About FastP Tool
Raw
Quality_control
Preprocessing
alignment
reads
1 day ago by
AIMAR
• 0
3
votes
9
replies
643
views
Transcript identification and quantification
splitseq
transcript
scRNA
23 hours ago by
anton.avramov
• 0
0
votes
1
reply
244
views
Treatment of nanoparticles after buying before the experiment
fermentation
treatment
Nanoparticles
dark
updated 4 days ago by
ATpoint
88k • written 4 days ago by
Nick
• 0
2
votes
1
reply
248
views
Tool:
Accessible color palettes for charts and dataviz
dataviz
updated 2 days ago by
Bastien Hervé
6.2k • written 5 days ago by
Pierre
▴ 20
3
votes
4
replies
394
views
Warning in bcftools when subsetting a VCF by variant ID
bcftools
VCF
Beagle5.5
updated 1 day ago by
Pierre Lindenbaum
166k • written 5 days ago by
Mwangana
• 0
1
vote
2
replies
291
views
Lucidea Array Spotter - Question about machinery
sequencing
Microarray
updated 5 days ago by
GenoMax
151k • written 5 days ago by
Taylor
• 0
0
votes
3
replies
375
views
Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
slingshot
PCA
Seurat
scater
single-cell
updated 5 days ago by
Bastien Hervé
6.2k • written 5 days ago by
txema.heredia
▴ 210
1
vote
1
reply
263
views
What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
motifs
atac-seq
factor
jaspar
transcription
updated 5 days ago by
GenoMax
151k • written 5 days ago by
Ambuj
• 0
0
votes
3
replies
355
views
How can I find KO IDs for ORF sequences in a large FASTA file?
KEGG
ORF
updated 5 days ago by
Ram
45k • written 5 days ago by
Nikesh
• 0
0
votes
0
replies
219
views
Single MAG Recruitment to multiple metaT Samples
metagenomics
rna-seq
transcriptomics
5 days ago by
zjhennin
• 0
0
votes
1
reply
1.1k
views
Normalization - Tissue specificity analysis
gtex
updated 6 days ago by
Pallavi
• 0 • written 4.1 years ago by
Filago
▴ 100
2
votes
4
replies
3.1k
views
Transcript Specific Expression Data
rna-seq
updated 6 days ago by
Pallavi
• 0 • written 12.5 years ago by
disco
▴ 30
9
votes
6
replies
8.0k
views
6 follow
Database To Look For Tissue-Specific Transcript Expression Of The Same Gene.
transcript
updated 6 days ago by
Pallavi
• 0 • written 12.2 years ago by
michealsmith
▴ 800
6
votes
6
replies
2.2k
views
6 follow
Tool:
Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/)
containers
docker
updated 2 days ago by
barslmn
★ 2.4k • written 6.2 years ago by
pegi3sdocker
▴ 10
1
vote
0
replies
304
views
Job:
Looking for a mentor
health
mentor
informatics
updated 6 days ago by
GenoMax
151k • written 6 days ago by
yoav.lama
▴ 10
0
votes
0
replies
468
views
Job:
Postdoc fellow - genetics, proteomics, single cell and bioinformatics, Indiana University, Indianapolis, USA
proteomics
genetics
cell
single
bioinformatics
updated 6 days ago by
GenoMax
151k • written 6 days ago by
Jingwen
• 0
0
votes
0
replies
242
views
Strand bias and placement bias in variant calls
Variant
filter
updated 6 days ago by
Pierre Lindenbaum
166k • written 6 days ago by
Carolyn
• 0
0
votes
0
replies
248
views
STARsolo for multiome GEX: trimming (--clip5pNbases) & whitelist handling
STARSolo
multiome
whitelist
clip5pNbases
6 days ago by
IrK
▴ 100
121,125 results • Page
1 of 2423
Recent Votes
Answer: Which additional files are needed for the -taxids option in blast?
Comment: Averaging multiple IgG BAM files for use as a control in ChromHMM
Comment: Averaging multiple IgG BAM files for use as a control in ChromHMM
Comment: Averaging multiple IgG BAM files for use as a control in ChromHMM
Answer: Deduplication rate of shotgun metagenomes using fastqc
C: Bowtie2 error with single end mapping
Gene Exons Painter
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CRISPYCC
• 0
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Recent Replies
Comment: Sequence Duplication for Single-End 3RAD Data
by
Sarah
• 0
Thank you for your reply! Do you think this might be due to trimming? Some of my samples have what FastQC categorizes as Illumina adapters …
Comment: Efficiently find regions in bed file that are within start and end regions of an
by
GenoMax
151k
Thank you for clarifying that. While there is `bedtools window` : https://bedtools.readthedocs.io/en/latest/content/tools/window.html it …
Comment: Efficiently find regions in bed file that are within start and end regions of an
by
rxs1018
• 0
I'm familiar with using bedtools for finding intersections, but my understanding is that it is only capable of computing intersection/fract…
Comment: Efficiently find regions in bed file that are within start and end regions of an
by
GenoMax
151k
`bedtools intersect` : https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html Curious as to how/why you did not find this …
Comment: Which additional files are needed for the -taxids option in blast?
by
WaspInSpace
• 0
Thank you very much, this worked! But carefull note for everyone doing the same thing: The more taxIDs you give `blastdbcmd`, the longer it…
Comment: Which additional files are needed for the -taxids option in blast?
by
WaspInSpace
• 0
Quick comment for everyone who plans to do this: For me, `blastdb_aliastool` wasn't able to do the job because the added databases (8 speci…
Comment: 16S Libraries With Non-Purified Short Fragments
by
GenoMax
151k
Please post at SeqAnswers.com or an experimental biology forum such as biology stackexchange. While you may get an answer, the question i…
Comment: How to map polyA tails to barcodes in paired end reads for single cell RNA-seq
by
GenoMax
151k
> then finding the corresponding barcodes in R2 I don't think that is possible .. unless the inserts are short and R2 reads into the barco…
Comment: Circular heatmap using circos.heatmap in R
by
Bastien Hervé
6.2k
What do you want to do ? vst_data = rbind(cbind(matrix(rnorm(50*5, mean = 1), nr = 50), matrix(rnorm(50*5, mea…
Comment: Averaging multiple IgG BAM files for use as a control in ChromHMM
by
ATpoint
88k
BAM files do not contain counts or an "average-able" metric so I would simply merge the files indeed, maybe after subsampling to the same r…
Comment: differential exon usage from Salmon outputs
by
n_navy
• 0
I see, thank you. So do you suggest using featureCounts instead?
Comment: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
by
luminea
▴ 10
Hi everyone, In my case, I have 3 IgG CUT&Tag BAM files (replicates) that I would like to use as a control in ChromHMM for modeling chroma…
Comment: Circular heatmap using circos.heatmap in R
by
Yukta
• 0
Thank you @Bastien Hervé I tried the same thing in my own way. The 'split' argument i tried using in circos.heatmap function only, it solve…
Comment: ValueError: Found array with 0 sample(s) (shape=(0, 138)) while a minimum of 1 i
by
shevch2009
• 0
Yes, in tutorial - metawrap binning -o INITIAL_BINNING -t 96 -a ASSEMBLY/final_assembly.fasta --metabat2 --maxbin2 --concoct CLEAN_READS/ER…
Answer: Editing and Adding to a GTF file
by
gernophil
▴ 120
I'm not exactly sure, if this works for your usecase, but maybe you could try PyRanges. `read_gtf()` and `to_gtf()` seem helpful here. Neve…
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