Fastq: how can I check if they are from DNA or RNAseq data?

Question

[svp]

I have (gave me) Illumina fastq files, which I want to use for variant calling, and I do not know if they are DNAseq or RNAseq data. How can I check this? I do not have any report or who to ask ?

Answer 1

[GenoMax]

Align them to the reference genome and check with a genome browser to see where the reads align. With good RNAseq data the reads should mainly align to exons, with DNAseq reads should more or less uniformly align to entire reference.

Answer 2

[Antonio R. Franco]

I guess after mapping against a genome you will see that quite a few reads map to introns. Use a non splicing-aware program, such as bowtie2, BWA or the like

A clue will be given by analyzing the level of duplication, because in RNA is much higher. Some poorly sequenced DNA however, can also have overrepresented sequences