alignement paired end reads to long reads

[mido1951]

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

[mido1951]

any response?!!!

[GenoMax]

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.

[mido1951]

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.

[GenoMax]

https://www.youtube.com/watch?v=lFT4a5XI_3Q
https://www.youtube.com/watch?v=zMAa9gFd2Gs
https://www.youtube.com/watch?v=2qGiw4MRK3c

http://bix.ucsd.edu/projects/blasr/ - See the reference for the paper.

[mido1951]

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?

[GenoMax]

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.

[mido1951]

Genomax thank you for your help.
You have helped me a lot.
Is there another person who knows the answer?