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Preprocessing :: Reference preparation

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Asia Mendelevich edited this page Aug 31, 2022 · 9 revisions

Recommendations of reference preparation for spike-ins processing:

Reference preparation per organism:

  • Creation of F1 VCF (ref=allele1 and alt=allele2, SNPs only)
  • Creation of allele1 pseudogenome

Same as for ASEReadCounter* ( Wiki: 1.Reference preparation, sections "Files needed at the very beginning of the analysis", "Preparing files for using as reference" and "Reference preparation").

Note: the only difference, we now don't need allele2/pat pseudogenome, created together with allele1/mat

Creating of pseudogenome chimeras for main and spike-in organisms:

  • Creating of joint allele1 fasta (org_main + org_spikein)
  • Creating of joint gtf (org_main + org_spikein)
  • Creating of joint F1 VCF (org_main + org_spikein)

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