TEs supported by long reads but with no short reads aligned

[yuyun-zhang]

Hi,

Thank you for the tool and insightful ideas!
I ran LocusMasterTE on my dataset, combining long-read and short-read quantification for TEs. However, I noticed that for some TEs supported by uniquely mapped long reads but lacking short-read support, their final counts are zero. Do you think we should consider rescuing those TEs?

Best,
Yuyun

[LEESojung1998]

Hi,

Thank you for your interest. Given that long-reads and short-reads are obtained from the same tissue or cell lines, rescuing them might be beneficial. However, LocusMasterTE is specifically designed to quantify short-read RNA-seq with any available long-read input. We believe rescuing uniquely mapped reads from long-reads might be risky if they originate from different cell types. Thus, we currently do not have the option to rescue reads that are uniquely mapped by long-reads.

Best,
Sojung

[yuyun-zhang]

Hi Sojung, thanks for your reply!