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cancerit / telomerecat

Telomerecat: The telomere computational analysis tool
GNU General Public License v3.0
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Extremely low read counts and telomere length #42

Open sbrt opened 2 years ago

sbrt commented 2 years ago

Hallo,

I have a WGS sample generated from an oral mucosa swap, sequenced with high coverage (150x) and mapped against GRCh38. Running telomerecat I get very low read values and a very low telomere length (see output below).

Sample,F1,F2,F4,Psi,Insert_mean,Insert_sd,Read_length,Initial_read_length,F2a,F2a_c,Length
XXXXX.bam,43,111,19,0.976,385.551,84.959,150,150,92,92,492.5

Any idea what could cause this?

Kind regards and thank you!

AndyMenzies commented 2 years ago

Hi

Samples with a depth of 150x tend to be whole exome or targeted sequencing. Has there been a selection step in the library generation process, or is this genuinely a 150x whole genome sample?

Andy

sbrt commented 2 years ago

It is WGS data and the coverage is quite even.

AndyMenzies @.***> schrieb am Mo. 25. Juli 2022 um 10:30:

Hi

Samples with a depth of 150x tend to be whole exome or targeted sequencing. Has there been a selection step in the library generation process, or is this genuinely a 150x whole genome sample?

Andy

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