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zhqingit / giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
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[fai_fetch_seq] The sequence "10" not found #56

Open JasminZarah opened 1 year ago

JasminZarah commented 1 year ago

Hi,

I'm having an issue after human genome alignment. I followed these steps before encounter this issue:

  1. index with bowtie2 (GRCh37)
  2. alignment without trimming
  3. samtools to create .sam file after sorting it.

This is the command that creates the issue:

$ samtools mpileup -E -uf GRCh37.genome.fa name_sorted.bam > name.mpileup

[fai_fetch_seq] The sequence "10" not found [fai_fetch_seq] The sequence "10" not found

How can I get the .vcf files? Am I use the genome index instead of the genome.fa?

Thanks a lot