equivalent of minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam ?

marbl / Winnowmap

Long read / genome alignment software

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equivalent of minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam ? #4

Closed TommySchooner closed 4 years ago

TommySchooner commented 4 years ago

Hi there,

I wonder if the software has any equivalent of the minimap2 minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam for the direct RNA sequencing data?

Thank you for helping!

cjain7 commented 4 years ago

Hi, I've added the splice option back. Please feel free to try it by pulling the latest code from master branch. In your command, since you are changing k-mer size from 15 to 14; you'd also need to revise meryl command accordingly.

meryl count k=14 output merylDB ref.fa
meryl print greater-than distinct=0.9998 merylDB > repetitive_k14.txt
winnowmap -W repetitive_k14.txt -ax splice -k14 -uf ref.fa direct_rna.fq.gz >  aln.sam

TommySchooner commented 4 years ago

Dear Chirag Jain,

Thank you very much for your kindly help! Sorry for my late reply since then! That helps a lot and would provide me with a lot help in the analysis! Really a big thank you!

Best regards,