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Question: Qc of Bisulfite Fastq file
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gravatar for rob.costa1234
9 months ago by
rob.costa1234 • 150
United States
rob.costa1234 • 150 wrote:

I have a bisulfite sequencing data and want to check the quality of the data generated. Is there any special tool for checking QC of bisulfite sequenced Fastq file or FASTqc will serve the purpose. I believe bisulfite seq is different from other sequencing we may have to use special QC tools. Any pointer or comments that Fastqc is Ok will be helpful. Thanks
bisulfite sequencing • 355 views
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modified 9 months ago by Sirus • 770 • written 9 months ago by rob.costa1234 • 150
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gravatar for Devon Ryan
9 months ago by
Devon Ryan ♦ 80k
Freiburg, Germany
Devon Ryan ♦ 80k wrote:

FastQC will work fine, just remember that some of the modules will show the dataset as having failed.
ADD COMMENT • link written 9 months ago by Devon Ryan ♦ 80k
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gravatar for Sirus
9 months ago by
Sirus • 770
Boston/USA
Sirus • 770 wrote:

At the fastq level, you cannot tell much I think, just the quality of the sequencing.

However, you can check some other metrics after mapping, such as the conversion rate (especially if you have a spike-in lambda genome). You can also check the mapped and un-mapped reads, the CpG and non-CpG site (generally non-CpG is very low except in neurons and embryonic steam cells).

if you use Bismark, you can check the summary reports. You can also use tools such as MethPipe to check the conversion rate.
ADD COMMENT • link written 9 months ago by Sirus • 770
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