Alignment of single/paired end reads with rsubread align

Question

[qstefano]

Hi biostars,

align function by Rsubread package allows to set parameters according to reads layout (single or paired), since i download fastq files from SRA, if the layout is paired, i obtain a single fastq files containing both pairs.

The question is: if i don't specify if fastq file is paired or not, align would detect "automatically" this and consequently align reads correctly? or align the reads as if it were a single layout?

any reply will be appreciated, thanks.

[GenoMax]

You can easily split the files using reformat.sh from BBMap suite.

reformat.sh in=input.fastq out1=R1.fq out2=R2.fq

You could have also used --split-files option with fastq-dump to get pair of files.

[Dunois]

@genomax just as an aside, would reformat.sh produce an empty R2.fq if the input is unpaired reads?

[GenoMax]

Yes. If inputs can't be recognized by /1 or /2 (old Illumina data) or 1:N: or 2:N: (current format) at the end of read headers.

[qstefano]

That's clear, thanks!

[ATpoint]

That is for interleaved files. Be sure that fastq-dump did not simply concatenate the mates into a single long read which it sometimes does. Confirm that you have one entry per mate otherwise alignment is going to be a mess.