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I used tophat2-cufflinks (latest version) to detect the transcripts and validate by experiments. I found one region (attached file, 100 bp length Hiseq, paired-end, human genome), cufflinks tends to merge the two genes together, which actually they are separated from each other by a small gap (might have several reads mapped). I wonder if there are parameters can control the distance and coverage for merging two closely transcripts.
the second question, is about the pre-mRNAs, it seems they are really prevalent detected by sequencing, I tried to change “-j/--pre-mrna-fraction ” to remove the two pre-mRNAs in the attached picture, but it did not work. Would you tell me what other options I can use to remove them?
Thank you so much for your advice.
the second question, is about the pre-mRNAs, it seems they are really prevalent detected by sequencing, I tried to change “-j/--pre-mrna-fraction ” to remove the two pre-mRNAs in the attached picture, but it did not work. Would you tell me what other options I can use to remove them?
Thank you so much for your advice.
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