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
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).