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Question: about compute and correct GC bias
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gravatar for xpnathakur
21 months ago by
xpnathakur • 0
xpnathakur • 0 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 • 638 views
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modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 21 months ago by xpnathakur • 0
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gravatar for Devon Ryan
21 months ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k 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 COMMENT • link written 21 months ago by Devon Ryan • 1.9k
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