Hi!

I would like to recover unmapped reads from bulk RNA-seq data (fastq files) using kallisto but it seems there is no output file to obtain this information (at least in the las version of kallisto?) Does anybody try this?

What other option could be? using Star and doing the genome index using a cdna.fg.gz file?

Thanks a lot!!

It's possible but unfortunately not super straightforward to extract the unmapped reads.

You can use the --num option when mapping reads using kallisto bus.

You then use bustools text -pf on the output.bus file. The read number (zero-indexed) of the mapped reads will be stored in the flags column (i.e. the fifth column). That will tell you which read numbers (zero-indexed) in the input FASTQ files mapped (all other reads are unmapped).

I'll put together a tutorial on how to do this (or perhaps a simpler workflow) at a later date.