Question: about compute and correct GC bias
gravatar for xpnathakur
9 weeks ago by
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 • 74 views
ADD COMMENTlink modified 9 weeks ago by Jennifer Hillman Jackson22k • written 9 weeks ago by xpnathakur0
gravatar for Devon Ryan
9 weeks ago by
Devon Ryan1.3k
Devon Ryan1.3k 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 9 weeks ago by Devon Ryan1.3k
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