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tlemane / kmtricks

modular k-mer count matrix and Bloom filter construction for large read collections
GNU Affero General Public License v3.0
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Does kmtricks consider read orientation ? #10

Closed hl-xue closed 2 years ago

hl-xue commented 3 years ago

Hello,

I have a question about kmtricks on pair-end RNA-seq data: if the two fastq files are in "reverse-forward" mode, i.e. the first fastq contains reverse reads and the second fastq contains forward reads, does kmtricks treate them specially (for example firstly reverse-complement the first fastq before counting k-mers) ?

Thanks and best wishes !

tlemane commented 3 years ago

Hello,

All files are processed in the same way without special consideration, except that kmtricks uses the canonical forms of k-mers.

hl-xue commented 2 years ago

Sorry, I just found I missed your reply 5 months ago... Thanks a lot ! Best wishes.