How to check quality of raw NGS sequence data using FastQC

[@kothuritarun9479]

What if the per base sequence quality is showing Red

[@thereality657]

Good explanation

[@bioinfobase3720]

Thanks and welcome

[@kumaridurga2824]

How to detect length of adaptor sequences?

[@troy00114]

I dont know how acurate you need it but if you look at Per base sequence content and you can see where the high peaks are at the beginning, that is the primers/adapter sequences. since these are the same for most reads. the adapter sequences will be 100% and your primers depend on the method. if you want to you can cut that part off in a FastQ trimmer. for exact properties of the adapter look at the QC report that came with the FastQ files.

[@samiramousavifard4751]

thank you so much. it was useful for me.

[@bioinfobase3720]

Glad to hear that

[@anuranjansinghrathore4018]

how to set coverage and all type of para meters during trimming the sequences

[@bioinfobase3720]

It depends on the aim of your study. If u want to find SNP marker then u need to keep the coverage high and the qc score should be more than 30. But if you study the differential expression then u can qc 20 also. So u need to review the literature and fixed the parameters based on ur aim.

[@anuranjansinghrathore4018]

Can get ur personal email

[@amanullahaman6070]

Thanks for your nice tutorial. could you kindly tell me plz, how can I do this on windows system?

[@shubhamharip5862]

Thankyou so much. Your video was quite helpful
Can I get your email id?