aligning multiple fasta files

Question

[zizigolu]

Hey biostars,

How I can align multiple fastq files on reference genome or I have to align them individually?

[verma]

Hey Hi Sarah,

There is a tool called fasta genome search or you can use blast there is a blast for searching a given database or sequence you can use that also.

[Ram]

I'm sorry, but how is this relevant to the question?

[zizigolu]

Hey Ram, yes you are right I also did not give him.

[zizigolu]

Thank you

Answer 1

[Ram]

You can definitely align multiple FASTQ files to a reference genome - I do it all the time. You'd ideally be able to pass as parameters pairs of PE fastq files and any number of SE fastq files. Check out the documentation of the alignment program you're using to figure out the exact method to pass multiple files.

[zizigolu]

Thank you

Answer 2

[vinay.baranwal]

Use STAR aligner. It's very efficient provided you have the RAM resources.

[zizigolu]

Thanks a lot