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Question: Sequence Duplication level
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gravatar for sonam.rani
8 months ago by
sonam.rani • 10
sonam.rani • 10 wrote:

Will the alignment be incorrect or will there be some problem with alignment if sequence duplication level is not good? Shall I move forward with the alignment or is there a way to correct/minimize it?
fastqc duplication read chip-seq • 502 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by sonam.rani • 10
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gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There could be a technical problem or this might just be how you decided to construct the library. You can probably proceed with mapping, but first, review what this FastQC module does and make a decision based on that information.

FastQC manual: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Galaxy tutorials: https://galaxyproject.org/learn/

  • NGS logistics - this is an introduction to Galaxy's functionality for the analysis of Next Generation Sequencing data.
  • ChIP-seq: A simple ChIP-seq experiment with two replicates - an example analysis for finding transcription factor binding sites. Note the 50-60% duplicated levels in the sample data, and the filtering step after mapping to screen out multi-mapping sequences (possibly shorter/non-specific reads).

Thanks! Jen, Galaxy team
ADD COMMENT • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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