Telomere counting from NGS data
- 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