Hi, I want to simulate the reads with positional bias, i.e. more reads located in 3 primer end of the transcript and less in 5 primer end, which situation is usually found in real RNA Seq data. Is there any parameter to help generate such kind of reads? Thanks!

 

 

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  1. Micha Sammeth

    Hi Maxy,

    to my knowledge reads can accumulate at the 3'-end of transcripts due to a protocol bias, e.g. reverse transcription (RT) by poly-dT primers, or it can happen accidentally when long molecules break during RNA extraction via capturing the poly-A tails of messengers. The simulator provides computational models for the former protocol-driven bias, and there are descriptions of some sample parameters and correspondingly obtained results (Fig.6C) of poly-dT primed RTs.

    Cheers!

    1. maxy

      Thanks a lot!

      Yes, I tried to specify the parameter RT_PRIMER with "PDT" and it seemed work.