Off topic:Extracting only reads overlapping with a feature

Question

[Florian BERNARD]

Hi everyone,

I am working on a RNA-seq dataset generated with direct-RNA sequencing technology and the reads are rather bad. Out of 170K reads, only 90K are overlapping with a feature (according to HTseq-count). I was wondering if there was an easy way to extract only those reads as the other ones do not really interest me ?

Thanks in advance !