Questions tagged [genome-sequencing]

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Extract reads from bam files by their @RG

How could I extract reads from bam files by their read groups @RG ?, I've got one file containing all reads for 5 samples, the SM is appears NONE, So, I want to extract each sample reads by the @RG ...
3
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1answer
58 views

Produce a single sequential FASTA sequence out of BAM

I'm having problems properly looking for a solution because I'm a layman in Bioinformatics not familiar with the terminology. I'm hoping you can nudge me in the right direction, please! Thank you very ...
3
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2answers
100 views

Separation of mixed plasmid DNA sequences post whole-plasmid sequencing

Imagine a DNA sample containing a mixture of different intact plasmids. These samples are sequenced using either MiSeq or HiSeq sequencing. Would it possible to assemble these plasmids post-sequencing ...
4
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1answer
172 views

What are 2D reads in the Oxford MinIon?

Reading the Mash: fast genome and metagenome distance estimation paper, I see the reference to "2d reads" notion under the minION context (a sequencing technique) e.g ...
2
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1answer
35 views

Generating basic dna sequences in R

Looking for some guidance. In an introductory bioinformatics class I am tasked with doing the following in R: Create the sequence ACTGACTG Generate a random string of nucleotides with equal ...
1
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1answer
27 views

Genotyping with Illumina HumanOmni1-Quad before whole genome sequencing

I read a paper about (whole genome sequencing analysis of 100 Southeast Asian Malays. It says "Prior to library preparation, each sample was genotyped on the Illumina HumanOmni1-Quad as an initial ...
3
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1answer
506 views

Can I run STAR without an annotation file?

I wish to use Rascaf to scaffold a fragmented draft genome. For this, I need to provide a BAM file of aligned RNA-seq reads and the draft genome. So, I indexed the draft genome with STAR like this: ...
1
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1answer
55 views

How to QC overamplified shotgun library?

I made some NEB ultra II whole-genome shotgun libraries with around ~200ng of template going into the indexing PCR step. The PCR was run for 13 cycles and I ended up having high library concentrations ...
7
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4answers
4k views

What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?

What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing? I am about to start a MinION run on my laptop. What should I consider when choosing my basecaller? ...
3
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1answer
86 views

Can the canu assembler output a fastq file of the final assembly just like HGAP4?

I have assembled some genome from Sequel PacBio data both with HGAP4 on the SMRT Link interface and using canu on the command line. The HGAP4 assembler outputs a fastq file of the final assembly such ...
7
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2answers
2k views

How do PCR duplicates arise and why is it important to remove them for NGS analysis?

I am trying to understand PCR duplicates in NGS analyses (actually whole-genome). I searched, and the best answer I found is in this blog. However I don't understand if I understood how PCR ...
13
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3answers
828 views

Publicly available genome sequence database for viruses?

As a small introductory project, I want to compare gene sequences of different strains of flu virus. Are there publicly available databases of flu virus gene sequences?
11
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2answers
4k views

Downloading a reference Genome for Bowtie2

How do I download a reference genome that I can use with bowtie2? Specifically HG19. On UCSC there are a lot of file options.
18
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4answers
472 views

Tools for simulating Oxford Nanopore reads

Are there any free open source software tools available for simulating Oxford Nanopore reads?