How to calculate depth and coverage？

[FAFUshiyan]

Hi,
How to get raw_cov.csv and exons_coordinates.bed ?

Best wishes,
Yan

[wkusmirek]

Hi,

if you have bam files, you must have also some file explaining the coordinates of the sequencing. This file in the repo is called exons_coordinates.bed. raw_cov.csv is a file that contain depth of coverage (samples in columns, number of rows equal to exons_coordinates.bed). The raw_cov.csv file must be generated on your own for eample using samtools bedcov.

Best wishes,
Wiktor

[FAFUshiyan]

Hi,
I receive the following error when performing normalization.

k = 2
Iteration 1 beta diff =0.45 f(GC) diff =0.00738
Error in glm.fit(x = c(-0.957928479357184, 0.386693467242366, 5.45207591997753, :
NA/NaN/Inf in 'x'
Calls: run_CODEXCOV ... normObj1 -> normalize -> glm -> eval -> eval -> glm.fit
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

[wkusmirek]

What is the coverage depth row where this error occurs? Is this the first row in your data?