RNA SEQ reads assembly for illumina sequenced data

Question

[Adyasha]

Hi everyone,

I have 10 paired end samples. I have done the quality check and trimming then I merged the trimmed reads and after that I have done the mapping using minimap2 using this command:

minimap2 -ax map-ont ref.fna(reference genome) trimmed.fq(merged trimmed reads) >aln.sam

I want to do the assembly now, but I don't find any tool where I can use this sam file

Please help me with this.

Thank you

[Trivas]

You have paired end reads from Nanopore?

[Adyasha]

sorry its from illumina

[Trivas]

What's your end goal? You should use programs like STAR, Salmon, Kallisto for mapping/generating count matrices.

[Matthias Zepper]

Then you probably shouldn't use the map-ont preset for Nanopore reads? And by merging, you mean you merged overlapping paired-end reads or you merged all 10 samples?

If your goal is a reference-guided de-novo assembly of the transcriptome, have a look at StringTie. Here are two tutorials (1,2) or you can use a ready-made pipeline with this capability.

[1769mkc]

just curious why do you need read assembly, is it known or unknown organism? why minimap2 in case of RNA-seq ?