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Combining microarray, RNA Seq, whole & exome sequencing
Microarray RNA
updated 3 minutes ago by 19k • written 2 hours ago by ▴ 60
6
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4
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265
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PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq padj p-value
updated 6 minutes ago by 19k • written 6 days ago by • 0
0
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1
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16
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Alternative Database for Somatic Indel Realignment (COSMIC Alternative)
COSMIC
updated 21 minutes ago by ▴ 20 • written 38 minutes ago by ▴ 80
0
votes
1
reply
44
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Minimap2 chimeric
reads chimerics minimap2
updated 52 minutes ago by ★ 2.0k • written 3 hours ago by ▴ 10
0
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0
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13
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incomplete data after running CreateSeuratObject in Seurat for scRNAseq data
scRNAseq
1 hour ago by Sara ▴ 260
0
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4
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48
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small RNA-seq length distribution of 100nt?
small-rnaseq fastp mirnas
updated 10 minutes ago by 142k • written 2 hours ago by ▴ 110
0
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1
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75
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Exome sequencing dataset for SKAT
SKAT VEP exome-sequencing
updated 3 hours ago by 162k • written 9 hours ago by ▴ 10
0
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0
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26
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Estimate/calculate power for two-sample Mendelian randomization?
MR
3 hours ago by huynguyenacademia • 0
0
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3
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177
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RNA-seq differentially expressed genes (DEGs) with low fold change values
DESeq2 RNA-seq DEGs ComBat_seq
updated 4 hours ago by 83k • written 14 hours ago by • 0
801
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167
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144k
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109 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 4 months ago by 2.8k • written 7.5 years ago by 100k
0
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0
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31
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Blog: Long-read single-cell Sequencing
RNASeq Long-read single-cell scRNA-Seq transcriptomics
5 hours ago by Gabby • 0
0
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0
replies
43
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TSS sites annotation for hg38
tss hg38 annotation
5 hours ago by octpus616 ▴ 100
0
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3
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122
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Cut&Run replicates handling
peakcaller replicates SEACR chipseq
updated 3 hours ago by 10k • written 9 hours ago by • 0
0
votes
0
replies
46
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kegg pathway analysis
_analysis metabolic_pathway Gibbs_energy_calculate
6 hours ago by yuxiang • 0
0
votes
1
reply
51
views
newbie question: why the length of adapter is not fixed?
Library construction Sequencing
updated just now by 142k • written 9 hours ago by ▴ 10
1
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2
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95
views
CNVnator Installation
CNV CNVnator WGS
updated 5 hours ago by 10k • written 10 hours ago by • 0
0
votes
0
replies
52
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InferCNV results interpretation
CNV inferCNV scRNA-seq
12 hours ago by Yingying • 0
0
votes
0
replies
53
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deeptools Compute reference-point and scale-regions
deeptools computeMatrix plotprofile
14 hours ago by RD ▴ 10
1
vote
5
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230
views
Creating a Seurat object with Visium public available data
Spatial Visium 10X
updated 15 hours ago by 44k • written 21 hours ago by • 0
4
votes
2
replies
645
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Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
updated 17 days ago by ▴ 330 • written 5 weeks ago by ▴ 30
1
vote
7
replies
289
views
Can I assemble chloroplast genome of plants using SRA data from NCBI and I can publish it ?
Chloroplast genome SRA
updated 14 hours ago by 100k • written 18 hours ago by • 0
1
vote
1
reply
122
views
Herald: The Biostar Herald for Wednesday, May 29, 2024
herald
updated 18 hours ago by 3.9k • written 19 hours ago by 2.8k
0
votes
1
reply
94
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enrichGO function produces NULL object
enrichGO
updated 19 hours ago by ★ 2.5k • written 20 hours ago by • 0
1
vote
2
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120
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Forum: How Can BioJobs Lab Effectively Attract Top Talent and Employers in the Biotech Industry?
biotech
updated 19 hours ago by ▴ 20 • written 21 hours ago by • 0
0
votes
1
reply
187
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vg call vs vg surject
vg variation graphs
updated 19 hours ago by ▴ 520 • written 4 weeks ago by • 0
2
votes
4
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2.0k
views
How do I create a gff(3) file from a genebank file?
gff genebank
updated 19 hours ago by 100k • written 3.2 years ago by ▴ 10
0
votes
0
replies
71
views
visualization of centromere
visualization centromere human
21 hours ago by kidpopaye • 0
1
vote
1
reply
150
views
Job: Seeking remote internship in genomic analyses
NGS genomics variant-calling
14 hours ago by SlowSD • 0
5
votes
9
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349
views
VG view and VG chunk failed when using SequenceTubeMap
vg vgteam
20 hours ago by gforg34 ▴ 20
4
votes
2
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120
views
cannot conda install macs3 on linux
atac macs3
21 hours ago by QX • 0
2
votes
5
replies
286
views
NCBI vs Ensembl - Ortholog genes Information
Genomics Orthologs NCBI Ensembl
updated 21 hours ago by ▴ 200 • written 1 day ago by ▴ 10
0
votes
2
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111
views
Chromosomal distribution of the trancscripts count
chrosome_location
updated 22 hours ago by 83k • written 22 hours ago by • 0
0
votes
4
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134
views
How to Split FASTQ File by UMI Indices into Multiple Files
SeqKit UMI split fastq
updated 21 hours ago by 142k • written 22 hours ago by ▴ 340
0
votes
1
reply
79
views
Alternatives RAST annotation
database alternative RAST annotation
updated 22 hours ago by 142k • written 22 hours ago by • 0
0
votes
0
replies
74
views
Job: Postdoctoral Fellow in Machine Learning for Neuroimaging Genomics at University of Otago – Dunedin, New Zealand
human-genomics machine-learning neuroimaging
23 hours ago by narun.pat • 0
6
votes
6
replies
210
views
Constructing single sequence genome assembly out of short reads
short reads assembly
updated 1 hour ago by 10k • written 1 day ago by ▴ 50
5
votes
8
replies
382
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse r
updated 23 hours ago by 83k • written 2 days ago by ★ 1.9k
3
votes
3
replies
196
views
RNA-Seq analysis
rna-seq
updated 1 day ago by ★ 2.5k • written 1 day ago by • 0
1
vote
5
replies
201
views
bcl-convert cannot create output directory structure at the path specified
illumina reads bcl-convert index demultiplexing
updated 23 hours ago by 142k • written 1 day ago by ▴ 10
0
votes
5
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222
views
Filtering reads that map to both references
bwa insertion alignment reference
updated 15 hours ago by ★ 1.8k • written 1 day ago by ▴ 180
0
votes
0
replies
74
views
Results of NOT FOUND encountered when running SCENIC
SCENIC
1 day ago by smilewang997700 • 0
4
votes
12
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1.0k
views
6 follow
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio DEG limma
updated 1 day ago by ★ 7.2k • written 15 days ago by • 0
0
votes
1
reply
114
views
monocle3 dot plot by groups and each cell types
monocle3 R
updated 1 day ago by 11k • written 1 day ago by ▴ 20
9
votes
12
replies
441
views
Set the same Y scale for different plots
ggplot2 R
updated 9 hours ago by 4.2k • written 1 day ago by ▴ 10
3
votes
1
reply
140
views
Intersection of multiple vcf files
isec vcf bcftools
updated 1 day ago by 22k • written 1 day ago by ▴ 30
4
votes
3
replies
251
views
when I use htslib to write a bam. Error of "truncated file" shows by samtools
bam htslib
updated 1 day ago by 142k • written 1 day ago by ▴ 10
0
votes
0
replies
85
views
Using a within population reference genome - Recombination
relernn vcf popgen recombination
1 day ago by dylan • 0
1
vote
0
replies
107
views
Why does WGCNA use weighted correlation instead of Pearson correlation?
wgcna
1 day ago by 絶望燃やし ▴ 10
0
votes
0
replies
91
views
reference geome gaf file obsolent GO replacement
gaf GO
1 day ago by Nicolas • 0
0
votes
1
reply
151
views
Can I count UMI-barcode combination without mapping?
HyDrop protein UMI UMI-Tools
updated 1 day ago by 142k • written 1 day ago by ★ 1.9k
117,203 results • Page 1 of 2345
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How to create an mzTab file (from MaxQuant data)?
2 PhD Students in single-cell bioinformatics
Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
Answer: How Can BioJobs Lab Effectively Attract Top Talent and Employers in the Biotech
Answer: Using samtools with GCS (google cloud storage) on a docker container seems to gi
Comment: Constructing single sequence genome assembly out of short reads
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Comment: Combining microarray, RNA Seq, whole & exome sequencing by i.sudbery 19k
Whole Genome and Whole exome are not gene expression technologies. They query the sequence of the genome, not the amount to which each is e…
Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad by May Ling • 0
![Seo et al. (2016), using p<0.05 to determine DEG][1] ---------- ![Liu et al. (2015), usnig p<0.05 and fold change to determine DEG][2…
Comment: small RNA-seq length distribution of 100nt? by GenoMax 142k
With smallRNA seq it is always better to find out the adapter used for making libraries based on kit. Then use that to trim the reads to re…
Answer: Alternative Database for Somatic Indel Realignment (COSMIC Alternative) by DGTool ▴ 20
One alternative that I have seen is the `simple_somatic_mutation_aggregated` VCF from the ICGC data portal: [here][1]. It's from the ICGC d…
Comment: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad by May Ling • 0
Dear swbarnes2, Thank you for sharing your opinion. I truly value your perspective and insights. However, I have come across some papers, s…
Answer: Minimap2 chimeric by dthorbur ★ 2.0k
Depending on what data you have and your expectations you might need to play around with parameters before `minimap2` starts mapping chimer…
Answer: Combining microarray, RNA Seq, whole & exome sequencing by Asaf 10k
The path I would choose is run the analysis with each technology separately and then combine the results with a meta-analysis. I would also…
Comment: small RNA-seq length distribution of 100nt? by Asaf 10k
So you should have a length of 50 for R1 and 50 for R2, how comes you have 101? Can you paste a few lines from your fastq files?
Comment: small RNA-seq length distribution of 100nt? by karlaarz ▴ 110
They performed 50 cycles and used the NovaSeq 6000 platform. I'd asked about the RNA length as I don't have that info yet.
Comment: small RNA-seq length distribution of 100nt? by Asaf 10k
How many cycles did you run? Did you measure the RNA length (the actual molecules, not the reads)?
Comment: Constructing single sequence genome assembly out of short reads by Asaf 10k
So why not do a reference-guided assembly?
Comment: Difference between proper paired reads and mapped and paired reads by Pierre Lindenbaum 162k
sorry, I deleted everything.
Comment: GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment by Maha • 0
I had the same issue: your fix worked for me too - thanks!
Comment: Constructing single sequence genome assembly out of short reads by analyst ▴ 50
1. Its bacteria 2. I want to align the reads against assembled genome and compare the results with reference genome alignment
Comment: Difference between proper paired reads and mapped and paired reads by QX • 0
can you share the slide again?
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