While trimming the adaptor and low quality RNA-Seq illumina paired end reads in Trimmomatic, I have got more Forward only survive of about 40 to 50%. This study is for estimate the transcript abundance (DEG) at various condition. How is the possibility to continue further...
1. USE singleton reads (R1-For only)
or
2. Only use both paired (survive) high quality reads (50% of the reads)
Any suggestion, Thanks in Advance
by, Ellango R.
You can ask your sequencing facility to redo the sequencing. In the sequencing contract it should have been mentioned that what would be the minimum good quality data they will provide.
Yes, definitely try to get them to redo the sequencing.
If that option falls flat, you have to weigh suggestion 1 and 2 against each other.
And check again how the average read quality is, and what concrete trimming parameters you used, maybe you can actually loosen the trimming parameters a bit
It can also help to merge reverse and forward reads, if there is an overlap of R1 and R2 sequences with and okay quality
Thanks Abhijeet & Sonja.
After I deeply check the data. Forward has more over represented sequence of Illumina nextra adaptor/Index and Reverse has highly over represented by Poly (G) sequence. Finally we dropped this data and asked the vendor to redo the sequence.
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