Read Length

[Young-Matthew]

Atlas-CNV/convert_GATK_DoC.R

Line 39 in 673a8e7

num_of_reads_in_exon = t(t(rrr)*exon_lengths) / 100

Dear authors,
Could you tell the reason that you choose 100 as the average read length? I got data that was sequenced by pair-end mode, is it ok to use 100? Thanks a lot

[theodorc]

Thank you for your interest in Atlas-CNV.

100 bp is not the average read length but the actual read length of the sequencing. We used paired-end reads from Illumina HiSeq 2500. If you use a different Illumina instrument like novaseq at 150 bp reads, then you ought to replace 100 with 150 in line 39.

It is noted to make this an option for next version.

Ted