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Old 04-22-2020, 02:20 PM   #1
Junior Member
Location: San Francisco, CA

Join Date: Sep 2011
Posts: 4
Default Trimming Fastq Reads for kallisto

Does kallisto match reads that are below that of the K-mer length used to
create the index? For example, the default K-mer value for creating the index
for kallisto is N=31. If I set trimmomatic MINLEN=20 and I get some reads
trimmed to < 31 bases, are these tested against the hash of 31 bases within
the index and not found (inefficient, tested but not counted), ignored because
they are too small for the K-mer length (inefficient, tested for length and
ignored), or matched as a substring of the K-mer within the index and counted
(flexible, some amount of mismatch allowed)?
Paul N. Hengen, PhD
Paul_N_Hengen is offline   Reply With Quote

kallisto, trimmomatic

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