Question: about compute and correct GC bias
0
gravatar for xpnathakur
14 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 • 419 views
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson24k • written 14 months ago by xpnathakur0
1
gravatar for Devon Ryan
14 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k 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 14 months ago by Devon Ryan1.9k
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