Hi everyone,
I'm about to perform a transcriptome assembly with Trinity, but I have a basic question.
I have two RNA-Seq files containing 40 million Pair-End reads from Illumina Hi-Seq. After performing a FastQC I’ve observed that the first 10 bases have a bad result in the "Per Base Sequence Content" plot and I want to trim them (by trimming I mean Trimming by column, because the quality trimming didn’t fix the problem) to avoid problems during the assembly. My problem is that I don’t know if by trimming the first 10 bases of the 5’ end in both files I will mess up the sequence pair mating and completely ruin the downstream analysis.
Could anybody help me with this? I know is a basic question, but I’m a newbie and I haven’t been able to get the answer by myself.
I'm about to perform a transcriptome assembly with Trinity, but I have a basic question.
I have two RNA-Seq files containing 40 million Pair-End reads from Illumina Hi-Seq. After performing a FastQC I’ve observed that the first 10 bases have a bad result in the "Per Base Sequence Content" plot and I want to trim them (by trimming I mean Trimming by column, because the quality trimming didn’t fix the problem) to avoid problems during the assembly. My problem is that I don’t know if by trimming the first 10 bases of the 5’ end in both files I will mess up the sequence pair mating and completely ruin the downstream analysis.
Could anybody help me with this? I know is a basic question, but I’m a newbie and I haven’t been able to get the answer by myself.
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