Question: Qc of Bisulfite Fastq file
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gravatar for rob.costa1234
15 months ago by
rob.costa1234150
United States
rob.costa1234150 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 • 502 views
ADD COMMENTlink modified 15 months ago by Sirus770 • written 15 months ago by rob.costa1234150
0
gravatar for Devon Ryan
15 months ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

FastQC will work fine, just remember that some of the modules will show the dataset as having failed.

ADD COMMENTlink written 15 months ago by Devon Ryan86k
0
gravatar for Sirus
15 months ago by
Sirus770
Boston/USA
Sirus770 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 COMMENTlink written 15 months ago by Sirus770
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