Pseudoalignment for repetitive sequences
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Shu Yi • 0
Last seen 11 weeks ago
United States

We have RNASeq data about human short tandem repeat satellites, and we are currently using kallisto as our aligner. We are concerned that kallisto might struggle with high repeat sequences, and we've tried decreasing the number of kmers from the default of 31 to 21 and 25. Does anyone have experience with using kallisto or other pseudo-aligners on high repeat sequences? or what might be the best aligner for high repeat sequences? ```

Kallisto RNASeq pseudoaligners ShortTandemRepeats • 112 views
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Last seen 39 minutes ago
United States

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