I sequence some reads based on the Directional RNA-Seq Protocol by using the example .par file, and I notice that by checking the .pro file generated, I can know which transcript is sequenced, and by checking the .gtf file, I can know all the exons related to the transcript. However, sometimes the transcript is lowly sequenced(by checking the "Covered Fraction"), and some of the exons related to this transcript is not sequenced. So I want to know is there a way to check whether an exon is sequenced or not directly? Thank you very much.


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  1. The best way to find out the exon is probably by overlapping the coordinates of the exons with the coordinates of the read in the .BED file. If you want to know from which transcript the simulated read came, you can check the read identifier: 4.5.2 - Read Identifiers