Question about CDS bases.

Question

[mangfu100]

Hi.

I am using TCGA data for my research. in TCGA data , I have often seen a term that CDS coverage.

for example, the below chart is TCGA data which shows the CDS coverage.

there are four rows and CDS coverage is 9th column.

Center    Tumor Sample Barcode     Reads          Total Gb    CDS Cov³20x    Normal Sample Barcode    Reads          Total Gb     CDS Cov³20x     Included in CNA Analysis?
WU        TCGA-04-1332-01A-01-1    183,967,266    16.5        77.68%         TCGA-04-1332-10A-01-1    186,242,236    19.3         84.72%           Y
WU        TCGA-04-1336-01A-01-1    110,961,984    11.1        77.98%         TCGA-04-1336-11A-01-1    113,547,422    11.4         78.26%           Y
WU        TCGA-04-1343-01A-01-1    187,456,234    17          82.35%         TCGA-04-1343-10A-01-1    166,927,742    17.3         76.95%           Y
WU        TCGA-04-1346-01A-01-1    120,675,386    12.1        74.75%         TCGA-04-1346-11A-01-1    112,711,208    11.3         70.99%           Y

Generally, we exclude samples with <50 % of target CDS bases covered at greater than 20-fold.

I think this means that we exclude the sample with less than 50 percentages of total which have also > 20 read counts.

Is that right?

Answer 1

[Devon Ryan]

Correct. The other way of saying this is, "we look at the 'CDS Cov 20x' column and get rid of samples with <50% there."

[mangfu100]

Thank you for your reply. But i already understood the statement. CDS concept is that i want to know.

[Devon Ryan]

Ah, CDS=coding sequence.