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jasonwong-lab / LocusMasterTE

Integrating long read sequencing enhances short read-based locus-specific transposable element quantification
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TEs supported by long reads but with no short reads aligned #1

Open yuyun-zhang opened 1 day ago

yuyun-zhang commented 1 day ago

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 commented 1 day ago

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