Hello all,
I am a newbie to NGS analysis. I recently got raw sequenced data (Illumina) for yeast.
Read length is 104 bps. I have average knowledge in R. I used ShortRead package for initial processing of reads. However I have some doubts/queries regarding adapter trimming. I searched many threads here and came to know about lot of trimming tools including these. According to many Trimmomatic found to be the best. Now I want to use this tool on my data. But this tool requires a fasta file (The Adapter Fasta) containing adapter sequence. Now,
1. How to know the adapter sequence??
2. My data is paired end reads, in this case how do I proceed??
How do I create this file?
I know my questions are too lame/simple for this forum and I am extremely sorry for such noob questions.
Help me.
Thank you.
I am a newbie to NGS analysis. I recently got raw sequenced data (Illumina) for yeast.
Read length is 104 bps. I have average knowledge in R. I used ShortRead package for initial processing of reads. However I have some doubts/queries regarding adapter trimming. I searched many threads here and came to know about lot of trimming tools including these. According to many Trimmomatic found to be the best. Now I want to use this tool on my data. But this tool requires a fasta file (The Adapter Fasta) containing adapter sequence. Now,
1. How to know the adapter sequence??
2. My data is paired end reads, in this case how do I proceed??
How do I create this file?
I know my questions are too lame/simple for this forum and I am extremely sorry for such noob questions.
Help me.
Thank you.
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