Question: Question about CDS bases.
0
gravatar for mangfu100
4.4 years ago by
mangfu100640
Korea, Republic Of
mangfu100640 wrote:

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 bold text.

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

16.50

77.68%

TCGA-04-1332-10A-01-1

186,242,236

19.30

84.72%

Y

WU

TCGA-04-1336-01A-01-1

110,961,984

11.10

77.98%

TCGA-04-1336-11A-01-1

113,547,422

11.40

78.26%

Y

WU

TCGA-04-1343-01A-01-1

187,456,234

17.00

82.35%

TCGA-04-1343-10A-01-1

166,927,742

17.30

76.95%

Y

WU

TCGA-04-1346-01A-01-1

120,675,386

12.10

74.75%

TCGA-04-1346-11A-01-1

112,711,208

11.30

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 it right?

snp genome • 1.0k views
ADD COMMENTlink modified 4.4 years ago by Devon Ryan87k • written 4.4 years ago by mangfu100640
3
gravatar for Devon Ryan
4.4 years ago by
Devon Ryan87k
Freiburg, Germany
Devon Ryan87k wrote:

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

ADD COMMENTlink written 4.4 years ago by Devon Ryan87k
Thank you for your reply. But i already understood the statement. CDS concept is that i want to know.
ADD REPLYlink written 4.4 years ago by mangfu100640

Ah, CDS=coding sequence.
 

ADD REPLYlink written 4.4 years ago by Devon Ryan87k
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