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Showing top results for tag: sequencing • reset
0
votes
2
replies
236
views
Inquiry about depth of coverage and copy number variation
number copy CNV sequencing depth variation
10 hours ago by Chen • 0
1
vote
2
replies
185
views
De novo assembly with more genome size than expected
illumina sequencing assembly genomics
updated 1 day ago by 146k • written 1 day ago by • 0
0
votes
2
replies
201
views
Why use Hi-C and/or Bionano for scaffolding when Nanopore sequencing exists?
wgs hic sequencing nanopore genomics
updated 1 day ago by ★ 1.4k • written 2 days ago by ▴ 10
0
votes
0
replies
190
views
Facing problems in analysis of bisulfite sequencing data
sequencing Bisulfite
updated 21 days ago by 146k • written 21 days ago by • 0
0
votes
0
replies
218
views
Is this phasing result normal?
haplotyping sequencing phasing nanopore
5 weeks ago by njornet ▴ 20
0
votes
0
replies
223
views
how to make a recombination map using a family of a diploid bee "mom" and 5 haploid "sons"
sequencing recombination-map
updated 6 weeks ago by 44k • written 6 weeks ago by • 0
2
votes
2
replies
396
views
Forum: A guide for beginners in bioinformatics
sequencing ngs
updated 6 weeks ago by 44k • written 6 weeks ago by • 0
11
votes
10
replies
10k
views
Duplicates In The Context Of Deep Sequencing
sequencing duplicates
updated 8 weeks ago by ▴ 10 • written 11.9 years ago by ★ 4.1k
0
votes
1
reply
294
views
Shift in GC content between forward and reverse reads in ddRADseq data
ddRAD sequencing fastQC ddRADseq
updated 8 weeks ago by 146k • written 8 weeks ago by • 0
1
vote
1
reply
377
views
Controlling for Baseline Taxa Relative Abundance [Longitudinal 16S rRNA Sequencing Data]
QIIME 16SrRNA Sequencing ANCOMBC-2
9 weeks ago by bjeremy • 0
1
vote
10
replies
788
views
ncRNA database for mus
contamination ncRNA sequencing
updated 9 weeks ago by ▴ 410 • written 9 weeks ago by ▴ 40
0
votes
1
reply
213
views
Isoforms and Transcriptome assembly with direct RNA Nanopore reads
isoforms assembly transcriptome sequencing nanopore
updated 10 weeks ago by 146k • written 10 weeks ago by • 0
1
vote
3
replies
1.3k
views
Merged Reference Panel using WES data
sequencing imputation reference
updated 11 weeks ago by 146k • written 5.0 years ago by • 0
1
vote
1
reply
290
views
Testing for specific genes of whole RNA Sequencing
R DESeq2 Sequencing RNA
updated 11 weeks ago by 85k • written 11 weeks ago by ▴ 20
345
votes
94
replies
251k
views
59 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 12 weeks ago by 146k • written 13.8 years ago by 5.0k
16
votes
14
replies
14k
views
9 follow
Combining GSEA (Gene Set Enrichment analysis) and DEG (Differentially Expressed Genes) to confirm results together- is it a good idea?
RNA-Seq R sequencing
updated 27 days ago by • 0 • written 4.3 years ago by ▴ 30
0
votes
4
replies
441
views
Use alignment as reference genome to separate DNA from a mixed sample
human sequencing nanopore alignment
updated 3 months ago by 146k • written 3 months ago by ▴ 20
4
votes
5
replies
566
views
DESeq2 results vs. shrinkage results
Shrinkage DESeq2 Sequencing RNA
updated 3 months ago by 20k • written 3 months ago by ▴ 20
10
votes
6
replies
533
views
What should be the term, "insert" or "insert size"?
TLEN sequencing alignment
updated 3 months ago by 44k • written 3 months ago by ▴ 80
0
votes
2
replies
333
views
Small RNA Seq Data-Removing Adapters- Illumina GA2 instrument
Sequencing
3 months ago by jspe • 0
0
votes
0
replies
208
views
NO sequence type of bacteria revealed using mlst package
Assembly Sequencing Genomics
4 months ago by Mohamed Samir ▴ 30
0
votes
3
replies
502
views
Where does cellranger log its estimates for the input to DETECT_COUNT_CHEMISTRY?
cellranger sequencing single-cell
updated 4 months ago by 85k • written 4 months ago by ▴ 300
3
votes
5
replies
590
views
Unable to retrieve the "Assembly method" of an assembly using Edirect in the terminal
Assembly Sequencing Genomics
4 months ago by Mohamed Samir ▴ 30
0
votes
1
reply
334
views
Comparing Gene Expression Before and After Treatment Using Nanopore Sequencing Data
sequencing normalisation nanopore
4 months ago by Dim • 0
0
votes
0
replies
200
views
Blog: Investigating male X heterozygosity in short read sequencing
heterozygosity nextflow sequencing chrX
4 months ago by barslmn ★ 2.3k
3
votes
4
replies
604
views
Overrepresented sequence in reverse read
FastQC Genomics Trimmomatic Sequencing ATAC
4 months ago by Jaskaran Singh • 0
4
votes
2
replies
467
views
NGS Data Analysis
NGS Genome sequencing
updated 4 months ago by ▴ 350 • written 4 months ago by ▴ 10
2
votes
4
replies
1.3k
views
Need to create a small artificial SRA file for unit testing
sequencing sequence
4.7 years ago by Sean McCorkle ▴ 20
0
votes
0
replies
233
views
Value of short kmer lengths with 300PE sequencing
metagenomics sequencing spades microbiome
4 months ago by Bryan ▴ 10
0
votes
4
replies
394
views
Estimating haplotypes from sequencing reads
sequencing reads haplotypes
4 months ago by Arline • 0
1
vote
2
replies
288
views
Sequece Raw Data QC A/T.G.C Distribution
illumina sequencing FastQC
updated 5 months ago by 146k • written 5 months ago by ▴ 120
2
votes
1
reply
294
views
Trimming from 151bp to 65bp
sequencing data
updated 5 months ago by 146k • written 5 months ago by ▴ 60
0
votes
2
replies
361
views
newbie question: why the length of adapter is not fixed?
Library construction Sequencing
5 months ago by Dora ▴ 10
2
votes
0
replies
518
views
Job: Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics Sequencing Sweden Stockholm SciLifeLab
5 months ago by Matthias Zepper 4.9k
1
vote
1
reply
286
views
Generating Group/Cluster Lists from fastq files
Sequencing RNA-seq DNA-Seq
updated 5 months ago by 146k • written 5 months ago by • 0
0
votes
9
replies
1.1k
views
Duplicated reads (IDs) from nanopore sequencing
bam nanopore sequencing
5 months ago by njornet ▴ 20
0
votes
6
replies
2.5k
views
Copy number Variation analysis using conumee
R software error sequencing genome
updated 5 months ago by 146k • written 3.6 years ago by ▴ 10
0
votes
0
replies
262
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization illumina ngs sequencing
6 months ago by rustykb ▴ 20
4
votes
7
replies
741
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
5 months ago by Chen • 0
10
votes
14
replies
1.5k
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 5 months ago by 146k • written 6 months ago by • 0
4
votes
6
replies
4.1k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 6 months ago by ▴ 20 • written 10.1 years ago by ▴ 40
0
votes
8
replies
980
views
What does it mean single base resolution in sequencing?
SNP sequencing
updated 6 months ago by 4.5k • written 6 months ago by ▴ 10
3
votes
3
replies
582
views
Sequence read length shorter than flow cell specification
illumina NGS sequencing
updated 6 months ago by 14k • written 6 months ago by • 0
0
votes
0
replies
260
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
6 months ago by Sergio A.S. ▴ 10
0
votes
1
reply
381
views
Annotating a dataset with gnomAD v4 using Hail
Python Sequencing Hail Exome Annotation
updated 6 months ago by ▴ 40 • written 6 months ago by • 0
1
vote
1
reply
295
views
Help/Direction Needed for Data Analysis of RNA
Sequencing RNA-seq DNA-Seq
updated 6 months ago by ★ 6.9k • written 6 months ago by • 0
5
votes
2
replies
530
views
Forum: Bioinformatics: Where do I start
Sequencing
updated 6 months ago by 44k • written 6 months ago by ▴ 20
0
votes
6
replies
967
views
PacBio adapters in transcriptome assembly from short read data?
adapter transcriptome sequencing pacbio vecscreen
6 months ago by Dunois ★ 2.7k
1
vote
1
reply
401
views
How do I get the 3bp sequence on either side of a co-ordinate
SAM genomics sequencing
updated 6 months ago by 44k • written 6 months ago by • 0
0
votes
2
replies
369
views
fmols for nanopore library loading
nanopore sequencing libraryprep fmol LSK114
updated 6 months ago by 146k • written 6 months ago by ▴ 20
50 results • Page 1 of 1
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Comment: Finding Differential Phosphosites in TMT Phosphoproteomics Data
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
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Recent Replies
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data by king • 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation by Chen • 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once? by GenoMax 146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset by allingt • 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap by jared.andrews07 ★ 18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type by allingt • 0
What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis by allingt • 0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
Comment: WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendr by allingt • 0
Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation? by allingt • 0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
Comment: dittoHeatmap; adding column labels on the heatmap by Varun Gupta ★ 1.3k
any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA? by allingt • 0
What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
Answer: Using NumReads column of quants.genes.sf file to build DESeq2 input by i.sudbery 20k
One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
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