Sorry for asking this very basic question. I have paired-end RNA-Seq data. After initial adapter and quality trimming, I used Tophat for alignment. Later, I obtained the read count using HT-Seq from the alignment file.
My questions is: Can I also somehow obtain the length of the reads that were counted/filtered by HT-Seq? This would allow me to see the distribution of read length in the data.
Thanks in advance for any help.