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Showing top results for tag: Sequencing • reset
0
votes
0
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47
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Tool: Manticore: a software to extract the intermixed regions of subgenomes in hybrid species
mapping hybrid subgenome genomics sequencing
4 days ago by Macspider ★ 3.4k
3
votes
5
replies
1.1k
views
Does Last aligner only outputs the mapped reads to a bam file ?
assembly alignment sequencing next-gen genome
updated 4 days ago by • 0 • written 3.0 years ago by ▴ 130
0
votes
0
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82
views
Tool: Is there any handy online tool for genomic analysis and data visualization?
NGS analysis BI Bioinformatics Sequencing
4 days ago by Louise ▴ 130
3
votes
2
replies
1.1k
views
Why ATAC-seq/CUT&RUN need paired-end sequencing?
HiC sequencing
updated 7 days ago by • 0 • written 2.1 years ago by • 0
1
vote
1
reply
105
views
Multiple BAM files (ccs) input with Lima (PacBio)
Long read PacBio sequencing
8 days ago by aa9gj ▴ 10
0
votes
2
replies
1.6k
views
RSeQC python runtime errors for tin.py
RNA-Seq sequencing software error
updated 8 days ago by ▴ 10 • written 3.1 years ago by ▴ 20
1
vote
1
reply
113
views
Cell cycle gene list for Rat
RNA Seurat rat sequencing 10x
updated 9 days ago by 52k • written 9 days ago by • 0
0
votes
0
replies
69
views
Job: Postdocs @ New York City: Long Reads Epigenomics, Metagenomics and Transcriptomics
epigenomics splicing assembly sequencing microbiome
9 days ago by fanggang ▴ 100
0
votes
8
replies
609
views
Poly-G in head of read NovaSeq
sequencing
updated 10 days ago by • 0 • written 12 months ago by ▴ 50
3
votes
4
replies
255
views
Flye assembly, increased coverage results in decreased N50
Minion genome assembly flye sequencing
10 days ago by roger.huerlimann ▴ 10
7
votes
6
replies
488
views
What is the best practice for analysing single-cell data with low sequencing depth?
10X depth scRNA-seq Sequencing Seurat data
11 days ago by volkanergin ▴ 10
0
votes
1
reply
90
views
How to create partition file from concatenated phylip sequence?
alignment sequencing
updated 16 days ago by ★ 12k • written 16 days ago by • 0
0
votes
4
replies
212
views
Dealing with non overlapping reads
sequencing vsearch amplicon bioinformatic illumina usearch
11 days ago by Adrien.andre • 0
2
votes
1
reply
130
views
Percentage of on target reads in custom capture sequencing
coverage capture sequencing bam
updated 18 days ago by 137k • written 18 days ago by ▴ 50
0
votes
1
reply
124
views
What is the well-recognized standard of coverage uniformity
sequencing CNV depth uniformity coverage
updated 18 days ago by ★ 2.3k • written 18 days ago by ▴ 590
0
votes
1
reply
90
views
minimap2 aligning sequencing reads to barcodes
demultiplex nanopore sequencing minimap2
updated 23 days ago by 104k • written 23 days ago by • 0
0
votes
0
replies
65
views
Removing paralogs from multiple sequence alignments
sequencing BAM genomics comparative paralog
24 days ago by mglasena ▴ 30
0
votes
4
replies
216
views
Detection of heterozygous exon deletion by Sanger and Long-Range PCR
Sanger sequencing PCR Long-Range
12 days ago by dunia.aburizeg ▴ 20
5
votes
6
replies
933
views
issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?
r bioconductor alignment R sequencing
updated 26 days ago by ▴ 30 • written 2.1 years ago by ▴ 50
3
votes
2
replies
465
views
guppy graphic card
sequencing nanopore guppy cuda
updated 27 days ago by ▴ 20 • written 5 months ago by • 0
3
votes
2
replies
2.1k
views
tools for identifying mitochondrial-targeting sequence in different proteins
sequencing alignment mtp
updated 4 weeks ago by • 0 • written 6.0 years ago by ▴ 50
2
votes
6
replies
174
views
How to find overlapping coordinates of a gtf file
gtf-file sequencing genome annotation RNA-Seq
updated 4 weeks ago by 33k • written 4 weeks ago by ▴ 50
0
votes
0
replies
259
views
Job: Research assistants or postdoctoral fellows in computational biology/bioinformatics (UMass Medical School, Worcester, Massachusetts)
computational sequencing genetics genomics
updated 4 weeks ago by 34k • written 4 weeks ago by ▴ 10
0
votes
0
replies
69
views
Why are there two peaks in per sequence GC content plot from FastQC report?
distribution WGS sequencing GC Illumina
4 weeks ago by Meng • 0
10
votes
8
replies
405
views
PHRED scores and sequence errors
probability sequencing errors PHRED
5 weeks ago by Dunois ★ 1.2k
2
votes
2
replies
415
views
Available annotation file for the PacBio Iso-seq data
sequencing
updated 5 weeks ago by 104k • written 18 months ago by ▴ 180
0
votes
0
replies
150
views
Appropriate tool to deconvolute complex Sanger chromatograms in order to retrieve specific DNA barcodes
sequencing NGS sanger deconvolution clontracer clonality
5 weeks ago by l.beumers • 0
1
vote
4
replies
207
views
Problem with Deseq2
galaxy Deseq2 sequencing RNA-seq
updated 5 weeks ago by ★ 1.1k • written 5 weeks ago by ▴ 40
1
vote
2
replies
161
views
Look at Different Locus in the Bam File
Genome HG38 Rna-Seq Nanopore Sequencing
5 weeks ago by santos48 ▴ 30
0
votes
0
replies
78
views
HOMER annotatepeaks.pl
ChIP-Seq HOMER sequencing next-gen
5 weeks ago by jjp55 ▴ 20
0
votes
1
reply
90
views
samtools mpileup: error CRC32 failure
sequencing SNP genome next-gen gene
updated 6 weeks ago by 137k • written 6 weeks ago by • 0
4
votes
6
replies
703
views
Trim bam file reads to the same length
RNA-Seq genome sequencing next-gen
updated 6 weeks ago by ★ 6.0k • written 18 months ago by ▴ 30
4
votes
6
replies
3.2k
views
calculate ti/tv ratio in WGS data
sequencing ti/tv ratio
updated 6 weeks ago by • 0 • written 3.2 years ago by ▴ 10
1
vote
5
replies
909
views
convert sam into paf format
genome alignment sequencing assembly SNP
updated 6 weeks ago by ▴ 20 • written 7 months ago by • 0
0
votes
1
reply
99
views
Forum: What can you detect with PE150bp shotgun sequencing with 100X depth
sequencing
updated 6 weeks ago by ★ 2.3k • written 6 weeks ago by • 0
1
vote
4
replies
198
views
Forum: Is WGS reliable for larges indels and duplication?
sequencing
updated 6 weeks ago by ★ 3.1k • written 6 weeks ago by • 0
1
vote
1
reply
132
views
How to calculate the *necessary* sequencing depth for a SNP
sequencing SNP analysis depth statistics Sequencing
updated 6 weeks ago by ▴ 570 • written 6 weeks ago by • 0
1
vote
3
replies
278
views
bowtie mismatch 0 alignment output
sequencing bam sam bowtie rna-seq
updated 5 weeks ago by ▴ 150 • written 6 weeks ago by ▴ 10
2
votes
3
replies
190
views
Can we detect aneuploids with sequencing (WGS 30X)?
sequencing
6 weeks ago by vpsev3 • 0
3
votes
8
replies
1.1k
views
how to batch download SARS-CoV-2 sequences data from NCBI?
sequence sequencing
updated 6 weeks ago by 104k • written 7 months ago by ▴ 30
4
votes
2
replies
211
views
How do I count the real total reads from a fastq file?
NGS Fastq End Paired Sequencing
updated 6 weeks ago by ▴ 90 • written 6 weeks ago by • 0
3
votes
4
replies
316
views
Pair-End Sequencing Algorithm Confusion (Illumina)
Sequencing
updated 7 weeks ago by 10k • written 7 weeks ago by ▴ 110
0
votes
1
reply
183
views
what is the best tool to remove PCR duplicates from miRNA seq without UMI?
sequencing mirna-seq tools
updated 7 weeks ago by ▴ 150 • written 7 weeks ago by ▴ 90
0
votes
0
replies
123
views
Job: Postdoc Fellow @ New York: Long Reads, Alternative Splicing and Human Diseases
assembly sequencing RNA-Seq
7 weeks ago by fanggang ▴ 100
0
votes
1
reply
109
views
SICER2 (or EPIC) genomes
Genome EPIC ChIP-seq SICER Sequencing
updated 7 weeks ago by 52k • written 7 weeks ago by ▴ 20
0
votes
1
reply
209
views
How can i handle the multimapped reads?
assembly sequencing alignment
updated 7 weeks ago by • 0 • written 5 months ago by ▴ 30
1
vote
1
reply
103
views
Extract co-ordinate for iCLIP data?
sequencing linux RNA
updated 7 weeks ago by 88k • written 7 weeks ago by ▴ 30
0
votes
4
replies
197
views
deeptools 3.5 plotCorrelation
ChIP-Seq sequencing plotCorrelation next-gen deeptools
updated 7 weeks ago by 6.5k • written 7 weeks ago by ▴ 20
4
votes
4
replies
199
views
How much weights a million reads
sequencing
7 weeks ago by gubrins ▴ 80
2
votes
6
replies
521
views
Hello everyone whenever i run this command this error terminates the command. can someone please guide me
analysis artic sequencing Minion nanopore
6 weeks ago by mibtisamnasar • 0
50 results • Page 1 of 1
Recent Votes
Gene Set Enrichment Analysis
Answer: Would this laptop be sufficient for small dataset/sequence analysis?
Answer: What's the biggest thing you dislike about bioinformatics?
Comment: opening downloaded files from STRING protein network without R
Comment: What's the biggest thing you dislike about bioinformatics?
Gene Set Enrichment Analysis
Comment: Removing genes of Seurat object during integration pipeline
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Recent Replies
Answer: Would this laptop be sufficient for small dataset/sequence analysis? by Mensur Dlakic ★ 12k
16 GB of RAM will not cut it for any serious bioinformatics application these days. Doubly so if you choose to run Windows.
Comment: inquiry related to snpsift by Kevin Blighe 75k
I see - thanks. I am not sure that `SnpSift annotate` can do this, but you can first remove the original ID via `bcftools`, as follows: …
Answer: Forum: Job opportunities in Europe, with and without a PhD by Kevin Blighe 75k
South Africa? - very nice. I had been considering moving there, would you believe. There is no correct answer to your question, and one ca…
Comment: inquiry related to snpsift by rheab1230 • 0
the command: java -jar SnpSift.jar annotate dbSnp144.vcf variants.vcf > variants_annotated.vcf I am getting no error. the input file …
Comment: Displaying points which fall outside of the plot window in EnhancedVolcano by os306 ▴ 10
Hi there, just to follow up on this, I used your package to generate my volcano plots and got exactly what I was looking for. I now wish to…
Comment: inquiry related to snpsift by Kevin Blighe 75k
Hi, please show: 1. the command(s) that you are using 2. a sample of your input data 3. a sample of your output data 4. any status, wa…
Comment: opening downloaded files from STRING protein network without R by fionajcunningham • 0
thanks GenoMax I will try this sorry for delay in reply!! Fiona
Comment: What's the biggest thing you dislike about bioinformatics? by WouterDeCoster 45k
The alternative, constant off-by-one errors, aren't my idea of fun either :-)
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
Yeah, you can filter min_cells in Seurat with SCtransform. That would probably change the gene numbers in the SCT assay of the object. I u…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
Doesn't sctransform has a `min_cells` parameter that you could use here? It will only consider genes detected in at least `min_cells` cells…
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
I was thinking of making it an arbitrary cut off of 10 cells, Seurat's documentation uses 3 for reading in a single sample. I believe that …
Answer: How To Split A Bam File By Chromosome by etiennedanis • 0
With samtools v1.11, ```samtools view -b in.bam chr1 > out.bam``` did not work for me. But ```samtools view -b in.bam 1 > out.bam``` wo…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
What is a "few" cells? So how many? You would need to manually calculate the fraction of cells expressing a certain gene. Not sure in which…
Comment: I want to make a graph for conserved regions by sa.youssef • 0
Thanks so much, it is a great suggestion. may I ask you if you know a way to visualize the results of these data in my report? as we are wo…
Comment: Minfi - estimateCellCounts by Papyrus ★ 1.1k
I understand that you have whole blood samples and that's why you expect them to have more granulocytes? You could also try the [ENmix][1] …
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