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823 results • Page 1 of 17
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0
votes
2
replies
65
views
sequencing data from different samples in the Integrative Genome Viewer (IGV)
IGV VARIANT GEN
updated 1 hour ago by ▴ 40 • written 3 hours ago by • 0
0
votes
1
reply
382
views
Understanding gene level copy number data from TCGAbiolinks
CNV TCGA
updated 3 hours ago by • 0 • written 13 months ago by • 0
0
votes
2
replies
85
views
Error in blast+
Windows path blast error PowerShell
updated 1 hour ago by • 0 • written 6 hours ago by • 0
0
votes
5
replies
223
views
Which language use as a beginner in Bioinformatics and Computational genomics
genomics Bioinformatics Computational
updated 2 hours ago by 12k • written 19 hours ago by • 0
0
votes
1
reply
99
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq mapping
5 hours ago by bkffadia • 0
0
votes
1
reply
105
views
using RMA normalized microarray in Limma
GEOdatabase Microarray limma RMA
updated 9 hours ago by 78k • written 14 hours ago by • 0
0
votes
1
reply
117
views
Can't install hisat2 with miniconda
unix miniconda hisat2
updated 9 hours ago by 99k • written 18 hours ago by ▴ 30
0
votes
2
replies
123
views
RNA seq
Differential expression gene
updated 5 hours ago by 99k • written 9 hours ago by • 0
0
votes
0
replies
166
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
updated 10 hours ago by ★ 1.1k • written 3 days ago by ▴ 710
0
votes
0
replies
66
views
Should I perform eQTL colocalization for just one of eGenes at a time?
colocalization coloc eCaviar eQTL
22 hours ago by maximal_life ▴ 20
0
votes
1
reply
143
views
Dimensionality reduction on data sets with variable dimensions
PCA dimensionality_reduction RNA_secondary_structure
updated 1 day ago by ★ 25k • written 1 day ago by ▴ 80
2
votes
1
reply
155
views
KEGG DATABASE
DATABASE KEGG
updated 1 day ago by ★ 25k • written 1 day ago by • 0
4
votes
2
replies
192
views
Fastest way to convert BED to GTF/GFF with gene_ids?
gff convert bed gtf
updated 22 hours ago by ★ 3.4k • written 1 day ago by ▴ 110
4
votes
0
replies
227
views
Tool: NOEL: An extremely fast Non-Overlapping Exon Length calculator written in Rust
gene-annotation exon-length
1 day ago by alejandrogzi ▴ 110
2
votes
3
replies
682
views
Generate a sequence of specific length with a list of motifs and intersperse with spacers
python R perl motif sequence
updated 1 day ago by • 0 • written 2.5 years ago by ▴ 30
0
votes
3
replies
233
views
best BLAST hits - which criteria is more important?
blast
updated 1 day ago by ★ 25k • written 1 day ago by • 0
2
votes
4
replies
341
views
Is bisulfite-seq data from different studies comparable with each other?
Methylation
updated 1 day ago by • 0 • written 3 days ago by ▴ 20
0
votes
1
reply
172
views
Issue with genetic QC sex check
plink
1 day ago by kl ▴ 10
0
votes
0
replies
81
views
BioSQL Unable to remove database using server.remove_database
BioSQL biopython Mysql Python
1 day ago by Navindu • 0
1
vote
5
replies
338
views
Bioinformatics: what do you think of it in the next 20 years?
question Bioinformatics
updated 9 hours ago by 99k • written 1 day ago by • 0
0
votes
0
replies
90
views
bootstraped treemix show no migration event
Treemix Bootstrap
1 day ago by reza ▴ 300
0
votes
1
reply
165
views
Are 10x cellranger-arc ATAC bam files deduplicated?
singlecell 10x
updated 1 day ago by 13k • written 2 days ago by • 0
3
votes
6
replies
393
views
From TPM to raw counts
tpm Deconvolution rnaseq
1 day ago by Gama313 ▴ 120
0
votes
2
replies
203
views
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
replies
386
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
replies
258
views
Using metagenome assembly and binning to identify and mitigate contamination in a genome
genomes contamination metagenomics
updated 1 day ago by ★ 25k • written 2 days ago by • 0
0
votes
2
replies
1.5k
views
Does GNOMAD use all LOFTEE LoF filters?
loftee gnomad LOF ensembl vep
updated 2 days ago by • 0 • written 3.8 years ago by ▴ 50
0
votes
3
replies
779
views
"MethylKit" package for WGBS data
MethylKit WGBS
updated 2 days ago by • 0 • written 2.3 years ago by ▴ 20
4
votes
3
replies
305
views
GO categorization
Ontology Gene
updated 2 days ago by ▴ 290 • written 3 days ago by • 0
0
votes
0
replies
115
views
is there a way to set colors pallets for glMDSPlot(x)?
Glimma glMDSPlot
2 days ago by James • 0
0
votes
0
replies
289
views
Job: Postdoc in comparative genomics of plant-associated bacteria (Polytechnic University of Madrid, SPAIN)
evolution genomics mutation bacteria genomes
2 days ago by Alejandro • 0
0
votes
1
reply
358
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
updated 2 days ago by ▴ 410 • written 9 days ago by • 0
0
votes
1
reply
222
views
How to find node Postion and source(sample) ?
vg
updated 2 days ago by ▴ 410 • written 4 days ago by ▴ 20
0
votes
0
replies
126
views
Job: Assistant Professor: Molecular Biology
Biology Molecular UCSD
2 days ago by lta ▴ 10
0
votes
0
replies
105
views
Compute matrix skipping many regions stating not found in compute matrix output
computematrix Deeptools
2 days ago by Mehwish ▴ 10
0
votes
0
replies
163
views
How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
motifs promoters bioinformatics
2 days ago by shome ▴ 10
1
vote
1
reply
175
views
Finding human .vcf files online to download
human findvcf vcf
updated 2 days ago by ★ 3.4k • written 2 days ago by ▴ 10
0
votes
3
replies
293
views
Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom
RNAseq differential-gene-expession limma batch-effect
updated 11 hours ago by ▴ 20 • written 2 days ago by • 0
2
votes
4
replies
285
views
How Can I move the scattered dots more closer into the center of box ?
R Boxplots geom_jitter
1 day ago by ohtang7 ▴ 40
0
votes
1
reply
171
views
How to identify CG, CHG, or CHH from MeDIP data
MethylationStudy CHG CHH CG MeDIP
2 days ago by Tm ★ 1.1k
0
votes
0
replies
133
views
Significance of several BUSCO target IDs for the same gene
target_id sequence-ontology BUSCO duplication
2 days ago by CoLa • 0
0
votes
0
replies
139
views
Issue softclipping reads when they belong and don't belong to a common amplicon
Samtools softclip
2 days ago by ManuelDB ▴ 80
12
votes
6
replies
423
views
Problematic fastq files...How can we trust them?
fastq
2 days ago by blackadder ▴ 30
1
vote
3
replies
241
views
An incomprehensible error with R package gggenes
R gggenes visualize
updated 2 days ago by 78k • written 2 days ago by • 0
3
votes
2
replies
270
views
Should I scale all genes in single cell Seurat?
singlecell
2 days ago by synat.keam ▴ 80
0
votes
1
reply
179
views
doubt about usage of megahit
trinity megahit
updated 2 days ago by 99k • written 2 days ago by • 0
0
votes
0
replies
127
views
Osmotic permeability of water transport in aquaporins
permeability Osmotic transport Water
2 days ago by Peerzada • 0
0
votes
1
reply
184
views
DIAMOND tutorial
tutorial DIAMOND
updated 2 days ago by 136k • written 2 days ago by ▴ 10
0
votes
13
replies
979
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
votes
2
replies
269
views
Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
metabolomic bioinformatic
updated 3 days ago by 86k • written 3 days ago by • 0
823 results • Page 1 of 17
Recent Votes
Comment: Bioinformatics: what do you think of it in the next 20 years?
Comment: KEGG DATABASE
Answer: From TPM to raw counts
Answer: GENE ONTOLOGY FOR TOMATO-ITAG4.1 OR 4
Answer: From TPM to raw counts
Comment: From TPM to raw counts
NOEL: An extremely fast Non-Overlapping Exon Length calculator written in Rust
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Recent Replies
Comment: BLAST: overflow error by Makaylee • 0
Did you ever find a solution? I'm getting the same error code and am not sure what's wrong. Running blast+ 2.11.0 as well with a built-in d…
Answer: sequencing data from different samples in the Integrative Genome Viewer (IGV) by dunia.aburizeg ▴ 40
Check out their documentation on the official IGV website. There is also a YouTube channel for IGV that can be a good start.
Comment: Error in blast+ by Shahin • 0
Spaces are not much better in Linux either. Better never use spaces in naming files, and directories, and column names in SQL Database stru…
Comment: Which language use as a beginner in Bioinformatics and Computational genomics by rpolicastro 12k
awk is turing complete /s
Comment: sequencing data from different samples in the Integrative Genome Viewer (IGV) by rpolicastro 12k
Generally we don't provide answers for assignments here. As a *very* generic hint you can download the human reference and variants from pl…
Comment: Understanding gene level copy number data from TCGAbiolinks by bioinfo355 • 0
Were you able to get answer for your questions?
Answer: Error in blast+ by Mensur Dlakic ★ 25k
Joys of doing Bioinformatics on Windows, and consequently dealing with spaces in file and directory names. I suggest you move your datab…
Comment: Which language use as a beginner in Bioinformatics and Computational genomics by Mensur Dlakic ★ 25k
I assume here you mean the usefulness for common tasks such as file manipulation and pipeline creations. How would one do sequence assembly…
Answer: Which language use as a beginner in Bioinformatics and Computational genomics by Mensur Dlakic ★ 25k
There is no single language that is best suited for all areas of Bioinformatics. If one's main interest is RNA-seq, R will probably be more…
Comment: Which language use as a beginner in Bioinformatics and Computational genomics by Brian Bushnell 19k
It depends on specifically what you will be doing. But IMO the order of importance is Bash > Python > R.
Comment: Bam files generated with STAR cause a segmentation fault core dump error when us by bkffadia • 0
![Galaxy Command Line][1] [1]: /media/images/8c45586a-e3e3-46dd-b06b-a9788a6e
Comment: RNA seq by Istvan Albert 99k
there is no need to "average" anything, the point of replicates and RNA-Seq in general, is to measure the same thing several times and use …
Answer: Which language use as a beginner in Bioinformatics and Computational genomics by Istvan Albert 99k
I would say every scientist needs to know R - so if you don't know R it would serve you well to learn it. In my opinion Python is not we…
Answer: using RMA normalized microarray in Limma by ATpoint 78k
Arrays do not have counts. RMA-proceased data are fine. See limma user guide.
Comment: RNA seq by ATpoint 78k
What is the question? I assume you googled 'differential RNA-seq' and tried the obvious tools such as DESeq2 and limma?
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