Question: about compute and correct GC bias
0
gravatar for xpnathakur
4 months ago by
xpnathakur0
xpnathakur0 wrote:

Hello I am having a trouble running the compute GC bias on a BAM file aligned by BWA-MEM. The error showing is "This job was terminated because it ran longer than the maximum allowed job run time.". As because my reference genome has over 700K sequences, is it the source of problem. If it is then is there any way to solve this.

Thank you.

compute gc bias deeptools • 128 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson22k • written 4 months ago by xpnathakur0
1
gravatar for Devon Ryan
4 months ago by
Devon Ryan1.5k
Germany
Devon Ryan1.5k wrote:

The problem is the 700,000 sequences, which will make deepTools incredibly inefficient. There is no way to solve this. Frankly, with 700,000 sequences I would redo the assembly, since that's an excessive number of contigs.

ADD COMMENTlink written 4 months ago by Devon Ryan1.5k
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