this might be a very basic question but I gave it some thought and don't see a satisfactory answer.
Let's say I have a FASTQ file from a sequencing experiment. How can one quickly determine if the given library is strand-specific?
On a related note, how important is it for the alignment (either Tophat or Bowtie) to specify if the library is strand-specific, for both single-end and paired-end reads?
Thank you in advance.