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TelMe

Telomere counting from NGS data

Explanation of the output file

  • SAMPLE name of the sample
  • TARGET path to the bed file
  • CMD full command-line executed

These are the headers for data based on individual RG-tags, one line per RG-tag

  • RG rg-tag as in the bam file
  • ALL # of total reads examined
  • ONTARGET # of reads deemed on target
  • TELOMERE # of reads deemed telomeric
  • CHRM # of reads mapped to chrM
  • TEL-UNMAPPED # of reads deemed telomeric that were also unmapped
  • CNT_TEL_LEN # of telomere repeats counted
  • RTPMO-w/offt Relative-telomere (reads) per million off-target reads
  • RTPKM-w/chrM Relative-telomere per thousand chrM reads
  • RTPMO-w/offtCNT Relative-telomere (length) per million off-target reads
  • FRACTION_DUPS fraction of duplication
  • TELOMERE_SEQ_FOUND ordered list of relative fraction of all the subtelomeric repeats identified

At the last line, there will be a summary over all the RG-tags in the bam file

  • Sample name
  • MEAN+-SD represent the values in the adjacent columns for each calculated value for each of RTPMO-w/offt, RTPKM-w/chrM, RTPMO-w/offtCNT
  • Mean of all
  • SD of all
  • ONTARGET-RATE fraction of all the reads deemed on target
  • DUP-RATE fraction of all the reads marked as duplicates

And the last value is the ordered-list of subtelomeric sequences with relative fractions

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Telomere counting from NGS data

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