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PYSCENIC - full garbage collection
PYSCENIC SCENIC GRN CELL SINGLE
4.4 years ago by GiuliaAC ▴ 20
0
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0
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683
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How to find allele frequency for a list of eQTLs based on finish/EUR population?
frequency eQTLs allele
4.4 years ago by macsuejacques • 0
0
votes
0
replies
630
views
Genome assembly
illumina bam genome vcf assembly
updated 4.4 years ago by 90k • written 4.4 years ago by • 0
1
vote
1
reply
1.4k
views
How to extract the shortest and the longest isoform from Trinity.fasta file?
assembly fasta trinity
updated 4.4 years ago by 3.9k • written 4.4 years ago by ▴ 20
2
votes
9
replies
5.9k
views
Looping over a function in R, and needing a variable name to save output as unique files
r
updated 4.4 years ago by ▴ 390 • written 4.4 years ago by ▴ 140
1
vote
2
replies
897
views
how to splice a gene sequence
assembly
4.4 years ago by linqide0418 • 0
3
votes
1
reply
1.5k
views
Clarification on KEGG orthologs, why don't all have KEGG modules?
ortholog database kegg
updated 4.4 years ago by 3.9k • written 4.4 years ago by ▴ 750
4
votes
2
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1.6k
views
Subread-align: Properly-paired versus not properly paired
alignment subread subread-align RNAseq
4.4 years ago by rependo ▴ 40
2
votes
0
replies
879
views
Herald: The Biostar Herald for Tuesday, June 15, 2021
herald
updated 4.4 years ago by 20 • written 4.4 years ago by 3.7k
2
votes
1
reply
1.7k
views
Molecular docking
pdbqt docking sdf
updated 4.4 years ago by ▴ 940 • written 4.4 years ago by • 0
1
vote
4
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1.5k
views
Looking for dataset with scRNA-seq data for normal (non cancer, non iPSCs) but prolifirating cells human (may be mouse or other )
RNA-seq
4.4 years ago by Alexander ▴ 220
1
vote
1
reply
982
views
Interpret PCA as combinations of SNPs
PCA SNPRelate
updated 4.4 years ago by 36k • written 4.4 years ago by • 0
0
votes
1
reply
1.3k
views
Buffer Error with bwa index
hg19 index bwa
updated 4.4 years ago by 166k • written 4.4 years ago by ▴ 250
2
votes
1
reply
1.9k
views
getting a set of coverage/depth metrics for multiple regions
bedtools samtools
updated 4.4 years ago by 36k • written 4.4 years ago by ▴ 20
0
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8
replies
2.2k
views
Annotation of 100kb region
Annotation
4.4 years ago by bioinformatics.queries ▴ 70
8
votes
23
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6.1k
views
How to get the genes that contain the highest number of isoforms from a fasta file generated by trinity de novo?
assembly fasta trinity
updated 3.9 years ago by • 0 • written 4.4 years ago by ▴ 20
0
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3
replies
1.5k
views
Graphic in LEfSe
Graphic
4.4 years ago by pnmb.mbc20 • 0
0
votes
1
reply
1.5k
views
Matplotlib plot stops responding when trying to close it
python python3 ProDy matplotlib
4.4 years ago by Kevin ▴ 70
4
votes
3
replies
2.4k
views
picard MergeBamAlignment fails to merge ubam and bam
picard MergeBamAlignment GATK
4.4 years ago by Frieda ▴ 60
4
votes
5
replies
9.8k
views
6 follow
Where can I find mouse Gene MatriX file format (GMT)?
gene RNA-Seq next-gen
updated 4.4 years ago by ▴ 10 • written 7.9 years ago by ▴ 190
0
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0
replies
807
views
Add or make representative diagrams on the axes of a graph with R
graphs ggplot2 data visualization R
4.4 years ago by diego1530 ▴ 80
3
votes
9
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2.6k
views
Query regarding WGCNA module
WGCNA R RNA-seq
updated 4.4 years ago by ★ 90k • written 4.4 years ago by ▴ 30
0
votes
2
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1.5k
views
TCGA-BRCA download
BRCA TCGA
updated 2.7 years ago by 45k • written 4.4 years ago by ▴ 50
0
votes
0
replies
703
views
Genes in GO pathways
GO pathways
4.4 years ago by some1 ▴ 10
1
vote
2
replies
3.0k
views
annotate VCF file with LRG ?
LRG vcf annotation
updated 4.0 years ago by 45k • written 11.4 years ago by ▴ 600
1
vote
11
replies
3.3k
views
Blast 2.11 not blasting all sequences in a file?
blast
4.4 years ago by DNAngel ▴ 260
0
votes
5
replies
1.5k
views
Dock image for transcriptomics assembly
transcriptomics docker
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 50
0
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0
replies
2.3k
views
Why are there two peaks in per sequence GC content plot from FastQC report?
distribution WGS sequencing GC Illumina
4.4 years ago by Meng • 0
0
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4
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3.4k
views
Defining the threshold for reads and features
scRNA-seq
4.4 years ago by zizigolu ★ 4.4k
0
votes
1
reply
1.5k
views
import metaphlan3 output to Phyloseq
Phyloseq metagenomics MetaPhaln3 Genomics
updated 4.4 years ago by 3.4k • written 4.4 years ago by • 0
0
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3
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1.4k
views
`samtools depth` reports all positions though I don't indicate `-a` or `-aa`
samtools
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by ▴ 20
7
votes
2
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1.3k
views
Forum: Course on genome assembly and annotation
genomics
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 350
2
votes
13
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4.1k
views
pearson correlation between lncRNA and mRNA
pearson correlation R cor.test
updated 4.0 years ago by 45k • written 4.4 years ago by ▴ 40
4
votes
4
replies
2.3k
views
Generate QC report for STARsolo (html)
quality RNA-seq control STAR
updated 4.4 years ago by ★ 2.2k • written 4.4 years ago by ▴ 70
0
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4
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1.7k
views
gene expression databases
GEO high-throughput GEO2R
4.4 years ago by Zahra ▴ 110
0
votes
0
replies
957
views
Salmon Library Types
salmon RNA-Seq
4.4 years ago by aka ▴ 10
0
votes
7
replies
4.3k
views
Issues with genome indexing with bowtie2-build
bowtie2
updated 4.4 years ago by ▴ 80 • written 4.4 years ago by • 0
1
vote
1
reply
1.5k
views
Install STAR-Fusion inside Conda (Snakemake) fails
snakemake STAR-Fusion Conda
updated 4.4 years ago by 90k • written 4.4 years ago by • 0
3
votes
6
replies
2.5k
views
VEP chromosome name query
ensembl VCF annotation VEP
4.4 years ago by prasundutta87 ▴ 730
0
votes
5
replies
1.6k
views
AnalysingTopHat and Fast QC results
tophat FastQC RNA-seq
updated 2.7 years ago by 45k • written 4.4 years ago by • 0
0
votes
3
replies
1.6k
views
RNAseq analysis using EdgeR or Deseq2 for generating fold change graph
change fold RNAseq
4.4 years ago by najibveto ▴ 130
0
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0
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1.6k
views
Detect fusion genes from WES data
Fusion fusion WES genes
22 months ago by enes ▴ 40
2
votes
2
replies
1.6k
views
Should I subset my data before running EstimateDisp() in RNA-seq analysis ?
RNAseq edgeR EstimateDisp
4.4 years ago by Basti ★ 2.1k
5
votes
2
replies
1.3k
views
Annotation Mycoplasma genome using Prokka
Mycoplasma Annotation Prokka
4.4 years ago by A_heath ▴ 180
0
votes
3
replies
1.6k
views
Extract specific gene id from an annotation file
R RNA-seq Linux
updated 4.4 years ago by ▴ 940 • written 4.4 years ago by ▴ 30
3
votes
12
replies
4.0k
views
Amount of unique variants in VCF with linux terminal
variants unique VCF linux
updated 4.3 years ago by 45k • written 4.4 years ago by ▴ 10
3
votes
4
replies
1.5k
views
How to create boxplot with jitter points where one point is labelled
Boxplot script Labell Jitter R
4.4 years ago by Roland • 0
1
vote
3
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1.7k
views
Filtering duplicates with MACS2 after re-sequencing a sample to increase read depth
macs2 chip-seq
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
2
votes
5
replies
2.3k
views
UMAP and "equal" objects
visualization
updated 4.4 years ago by • 0 • written 4.4 years ago by ★ 3.0k
0
votes
2
replies
1.6k
views
Is the pileup value the ATAC-seq counts?
ATAC
4.4 years ago by cthangav ▴ 110
122,198 results • Page 633 of 2444
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Answer: Midpoint rooting IQTREE newick file moves node support around
Answer: Subsetting before QC in Spatial Transcriptomics
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Comment: Feature Counts vs Salmon quantification
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
Comment: ID unifiying across different datasets
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Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by michael.ante ★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome? by dthorbur ★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
Comment: How to improving 2-Nucleotide RNA-seq Mapping Accuracy by 2411110159 • 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies by 2411110159 • 0
Very helpful!
Comment: direct RNA long-reads alignment against reference genome by frarodmar17 • 0
Okay, thanks! I removed reads.fa and I used the index created with minimap2 in .mmi format. Is this correct?
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