Genomax thank you for your help.
You have helped me a lot.
Is there another person who knows the answer?
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I don't think we are going to solve this through a forum discussion such as this. You need to find a sequencing facility (and/or a computational biologist/bioinformaticist) at your institute/university and talk through your doubts with them in person.Leave a comment:
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Thank you for the links.
But none of the links does not answer my question.
I know the stages of alignment and I aligement process.
for example in the alignment sequences used to align sequence to another sequence.
But in case of paired end, we have three sequences: paired end (2 sequences) and another sequnce! we try to align paired end reads to the sequence(consensus for example or the long reads)!
how to do this ?? !!
My question is not found in either the articles.
can you help me?Leave a comment:
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Leave a comment:
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Thank you for your answer.
I know that there are aligners NGS that can do this job but I want to understand the principle of alignment of paired end to a long sequence reads as PacBio.
if for example I want to create an alignment tools.
My question is not found in the articles of NGS alignments programs.
This is why I know how it works.Leave a comment:
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Take a fasta representation of the PacBio reads (there is nothing special about PacBio sequence). Use any NGS aligner of your choice after constructing a suitable index providing the PE data files. NGS aligners are aware that the PE reads are sequences from two ends of the same fragment.Leave a comment:
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alignement paired end reads to long reads
Hello,
I have a paired end reads DNA from illumina. and I want to make an alignment of paired end reads on PacBio long reads.
how to do this alignment?
I know that there are alignment tools that can do this job but I want to try to create an alignment tool like this.
the problem is I have one Long reads file but I have two paired end reads file.
how to align the paired end reads on long reads? do I have to take foward.fq and reverse.fq (paired end) separetly?
Thank you
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Differential Expression and Data Visualization: Recommended Tools for Next-Level Sequencing Analysis
After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...05-23-2023, 12:26 PM -
Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.
Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...05-19-2023, 10:03 AM -
With new tools and computational resources being released regularly, it can be hard to determine which are best suited for the analysis process and which older tools continue to be maintained. In an effort to assist the sequencing community, we interviewed three highly skilled bioinformaticians about their recommended tools for several important analysis applications.
Quality control and preprocessing tools
“Garbage in, garbage out” is a popular...05-16-2023, 10:11 AM
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