Question: Proper regex to mark duplicates using Picard tools on SOLiD data
1
gravatar for Jordan
3.8 years ago by
Jordan1.0k
Pittsburgh
Jordan1.0k wrote:

Hi,

I'm having trouble removing duplicates using Picard tools on SOLiD data. I get a regex not matching error.

The reads have the following names:

22_758_632_F3

604_1497_576

124_1189_1519_F5

358_1875_702_F5-DNA

And I don't think Picard tools is able to pick these read names with its default regex.

I tried to change the default regex. This time it does not throw an error, but it takes too long and times out (out of memory). I suspect I'm not giving the right regex. Here is my command:

java -jar $PICARD_TOOLS_HOME/MarkDuplicates.jar I=$FILE O=$BAMs/MarkDuplicates/$SAMPLE.MD.bam M=$BAMs/MarkDuplicates/$SAMPLE.metrics READ_NAME_REGEX="([0-9]+)_([0-9]+)_([0-9]+).*"

Any help is appreciated. Thanks!

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Jordan1.0k
1
gravatar for Jordan
3.8 years ago by
Jordan1.0k
Pittsburgh
Jordan1.0k wrote:

I was able to fix the issue, by adding -Xmx16g and increasing the RAM size. Apparently the RAM was not sufficient.

ADD COMMENTlink written 3.8 years ago by Jordan1.0k
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