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Can't install hisat2 with miniconda
unix miniconda hisat2
1 hour ago by Ozymandeus ▴ 30
0
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29
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Which language use as a beginner in Bioinformatics and Computational genomics
genomics Bioinformatics Computational
2 hours ago by 2021ag7698 • 0
0
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0
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38
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Should I perform eQTL colocalization for just one of eGenes at a time?
colocalization coloc eCaviar eQTL
5 hours ago by maximal_life ▴ 20
0
votes
1
reply
98
views
Dimensionality reduction on data sets with variable dimensions
PCA dimensionality_reduction RNA_secondary_structure
updated 10 hours ago by ★ 25k • written 11 hours ago by ▴ 80
772
votes
164
replies
129k
views
107 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 8 weeks ago by 2.3k • written 7.0 years ago by 99k
1
vote
1
reply
112
views
KEGG DATABASE
DATABASE KEGG
updated 10 hours ago by ★ 25k • written 11 hours ago by • 0
4
votes
2
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130
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Fastest way to convert BED to GTF/GFF with gene_ids?
gff convert bed gtf
updated 5 hours ago by ★ 3.4k • written 12 hours ago by ▴ 110
4
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0
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203
views
Tool: NOEL: An extremely fast Non-Overlapping Exon Length calculator written in Rust
gene-annotation exon-length
12 hours ago by alejandrogzi ▴ 110
2
votes
3
replies
662
views
Generate a sequence of specific length with a list of motifs and intersperse with spacers
python R perl motif sequence
updated 15 hours ago by • 0 • written 2.5 years ago by ▴ 30
0
votes
3
replies
180
views
best BLAST hits - which criteria is more important?
blast
updated 10 hours ago by ★ 25k • written 18 hours ago by • 0
2
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4
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290
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Is bisulfite-seq data from different studies comparable with each other?
Methylation
updated 17 hours ago by • 0 • written 3 days ago by ▴ 20
0
votes
1
reply
146
views
Issue with genetic QC sex check
plink
20 hours ago by kl ▴ 10
0
votes
0
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61
views
BioSQL Unable to remove database using server.remove_database
BioSQL biopython Mysql Python
20 hours ago by Navindu • 0
0
votes
4
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237
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Bioinformatics: what do you think of it in the next 20 years?
question Bioinformatics
updated 4 hours ago by 136k • written 22 hours ago by • 0
0
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0
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67
views
bootstraped treemix show no migration event
Treemix Bootstrap
22 hours ago by reza ▴ 300
0
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1
reply
144
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Are 10x cellranger-arc ATAC bam files deduplicated?
singlecell 10x
updated 1 day ago by 13k • written 1 day ago by • 0
1
vote
6
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342
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From TPM to raw counts
tpm Deconvolution rnaseq
14 hours ago by Gama313 ▴ 120
0
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2
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179
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Low coverage whole genome sequencing reveal excess heterozygosity for multiple SNPs. How to filter?
lcWGS WGS heterozygosity
1 day ago by beausoleilmo ▴ 560
3
votes
3
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361
views
How to obtain data on the coordinates of the Exon region from UCSC
hg19 UCSC exon
1 day ago by ayasu • 0
2
votes
4
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230
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Using metagenome assembly and binning to identify and mitigate contamination in a genome
genomes contamination metagenomics
updated 1 day ago by ★ 25k • written 1 day ago by • 0
0
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2
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1.5k
views
Does GNOMAD use all LOFTEE LoF filters?
loftee gnomad LOF ensembl vep
updated 1 day ago by • 0 • written 3.8 years ago by ▴ 50
0
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3
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759
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"MethylKit" package for WGBS data
MethylKit WGBS
updated 1 day ago by • 0 • written 2.3 years ago by ▴ 20
4
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3
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281
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GO categorization
Ontology Gene
updated 1 day ago by ▴ 290 • written 2 days ago by • 0
0
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0
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95
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is there a way to set colors pallets for glMDSPlot(x)?
Glimma glMDSPlot
1 day ago by James • 0
0
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0
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172
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Job: Postdoc in comparative genomics of plant-associated bacteria (Polytechnic University of Madrid, SPAIN)
evolution genomics mutation bacteria genomes
1 day ago by Alejandro • 0
0
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1
reply
337
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The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
updated 1 day ago by ▴ 410 • written 8 days ago by • 0
0
votes
1
reply
203
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How to find node Postion and source(sample) ?
vg
updated 1 day ago by ▴ 410 • written 4 days ago by ▴ 20
0
votes
0
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103
views
Job: Assistant Professor: Molecular Biology
Biology Molecular UCSD
1 day ago by lta ▴ 10
0
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0
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86
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Compute matrix skipping many regions stating not found in compute matrix output
computematrix Deeptools
1 day ago by Mehwish ▴ 10
0
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0
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111
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How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
motifs promoters bioinformatics
1 day ago by shome ▴ 10
1
vote
1
reply
157
views
Finding human .vcf files online to download
human findvcf vcf
updated 1 day ago by ★ 3.4k • written 1 day ago by ▴ 10
0
votes
2
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217
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Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom
RNAseq differential-gene-expession limma batch-effect
1 day ago by fluke • 0
2
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4
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251
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How Can I move the scattered dots more closer into the center of box ?
R Boxplots geom_jitter
16 hours ago by ohtang7 ▴ 40
0
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1
reply
147
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How to identify CG, CHG, or CHH from MeDIP data
MethylationStudy CHG CHH CG MeDIP
1 day ago by Tm ★ 1.1k
0
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0
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110
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Significance of several BUSCO target IDs for the same gene
target_id sequence-ontology BUSCO duplication
1 day ago by CoLa • 0
0
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0
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120
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Issue softclipping reads when they belong and don't belong to a common amplicon
Samtools softclip
1 day ago by ManuelDB ▴ 80
12
votes
6
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398
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Problematic fastq files...How can we trust them?
fastq
1 day ago by blackadder ▴ 30
1
vote
3
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221
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An incomprehensible error with R package gggenes
R gggenes visualize
updated 1 day ago by 78k • written 1 day ago by • 0
3
votes
2
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244
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Should I scale all genes in single cell Seurat?
singlecell
1 day ago by synat.keam ▴ 80
0
votes
1
reply
159
views
doubt about usage of megahit
trinity megahit
updated 1 day ago by 99k • written 2 days ago by • 0
0
votes
0
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108
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Osmotic permeability of water transport in aquaporins
permeability Osmotic transport Water
2 days ago by Peerzada • 0
0
votes
1
reply
162
views
DIAMOND tutorial
tutorial DIAMOND
updated 2 days ago by 136k • written 2 days ago by ▴ 10
0
votes
13
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954
views
Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cell Ranger.
fixed-RNA-profiling chromium cellranger scFFPE
updated 2 days ago by ▴ 70 • written 6 weeks ago by ★ 1.8k
0
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2
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249
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Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
metabolomic bioinformatic
updated 2 days ago by 86k • written 2 days ago by • 0
2
votes
8
replies
714
views
6 follow
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 2 days ago by 78k • written 20 days ago by ▴ 10
0
votes
0
replies
131
views
How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?
assembly fasta genomics nanopore pacbio
2 days ago by O.rka ▴ 710
0
votes
1
reply
424
views
Loftee no splice site annotations
Loftee VEP
updated 2 days ago by • 0 • written 21 months ago by ▴ 90
1
vote
1
reply
204
views
Bulk and Single Cell RNA-seq online course
single_cell_RNA-seq bulk_RNA-seq online_course
updated 2 days ago by 13k • written 2 days ago by • 0
1
vote
1
reply
165
views
gene set enrichment analysis- by enrichGO
rna-seq GO enrichment
updated 2 days ago by 99k • written 2 days ago by • 0
0
votes
0
replies
118
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal mutation VCF TMB
2 days ago by luckyday1661 • 0
113,899 results • Page 1 of 2278
Recent Votes
NOEL: An extremely fast Non-Overlapping Exon Length calculator written in Rust
Comment: Fastest way to convert BED to GTF/GFF with gene_ids?
Answer: Fastest way to convert BED to GTF/GFF with gene_ids?
Comment: KEGG DATABASE
Answer: Fastest way to convert BED to GTF/GFF with gene_ids?
Fastest way to convert BED to GTF/GFF with gene_ids?
NOEL: An extremely fast Non-Overlapping Exon Length calculator written in Rust
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Comment: Bioinformatics: what do you think of it in the next 20 years? by GenoMax 136k
> what do you think of it in the next 20 years? It will be what people like you make of it (assuming you are just starting out and that is…
Comment: Fastest way to convert BED to GTF/GFF with gene_ids? by cmdcolin ★ 3.4k
thanks for making these great tools
Answer: Dimensionality reduction on data sets with variable dimensions by Mensur Dlakic ★ 25k
Not sure whether what you want to do will be informative. That aside, UMAP works with sparse data. Simply insert missing values for shorter…
Comment: KEGG DATABASE by Mensur Dlakic ★ 25k
It happens.
Comment: best BLAST hits - which criteria is more important? by Mensur Dlakic ★ 25k
If your goal is to find the most similar sequence to your references, you have a correct sorting order. The next two criteria should probab…
Comment: best BLAST hits - which criteria is more important? by min • 0
thank you for correcting me. What I actually did was run a search using mmseqs2 and diamond to find similar enzymes in a MAG for my referen…
Answer: Fastest way to convert BED to GTF/GFF with gene_ids? by alejandrogzi ▴ 110
This is probably a duplicated question from: [How To Convert Bed Format To Gtf?](https://www.biostars.org/p/64346/) [How to convert …
Comment: From TPM to raw counts by Gama313 ▴ 120
I will give it a try and I will report results! Thanks for your help!
Comment: Bioinformatics: what do you think of it in the next 20 years? by Mensur Dlakic ★ 25k
Complaining about format conversions is like a wet biologist complaining about Westerns to prove protein expression. It is tedious and has …
Answer: best BLAST hits - which criteria is more important? by Mensur Dlakic ★ 25k
There is no way to run BLAST using mmseqs2 and diamond. Maybe you mean that you compared sequences using mmseqs2 and diamond? > I need to …
Comment: Bioinformatics: what do you think of it in the next 20 years? by Istvan Albert 99k
10 years ago https://www.biostars.org/u/36/ told us: >I've been doing bioinformatics for about 10 years now. I used to joke with a friend …
Comment: From TPM to raw counts by Istvan Albert 99k
Now that I thought about it more, you'll need the total number of reads mapped to produce the normalization factor. You can undo the TPM o…
Comment: How Can I move the scattered dots more closer into the center of box ? by ohtang7 ▴ 40
You're right. I would get help from StackExchange sites and GPT
Answer: Is bisulfite-seq data from different studies comparable with each other? by NextGenSeek • 0
The efficiency of bisulfite treatment itself can differ significantly, so I would definitely not compare bisulfite-seq data from different …
Comment: Issue with genetic QC sex check by kl ▴ 10
After setting set-hh-missing, I have the following boxplot, where a F statistic of 0.91 corresponds to a female in my phenotypic dataset wh…
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