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GenomeRIK / tama

Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
GNU General Public License v3.0
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Repeatmasker on iso seq data. #116

Open shri1984 opened 11 months ago

shri1984 commented 11 months ago

Hi, Thanks for great tool. I started to use it, but then I realised that some people to use repeat masker to fish out interpersed repeat sequences. I did see in my data where few bases get hit to different families within the same iso seq in intervals. It is some time 50 % of the total reads belong to TEs. What should one do? many times less than 2% of bases from a query mapped to 3 different TE families. Any put how one should proceed?

Thanks, Shri