I am very new to metagenomics stuff. I have some Illumina HiSeq sequencing reads. I have 1 forward fastq file and 1 reverse fastq file. I also have 2 other files which happen to be index files.
How do I check, if my raw reads have indices still present in them and if so how do I remove them from my reads?
I know it cannot be done using trimmomatic.
TIA.
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tahsin56 •
Thanks. Yes, I have 2 separate index files for my reads. What should I do with those? Are they somehow necessary in the assembly or quality trimming? TIA.
Not sure what software you are going to use for downstream analysis but here is the workflow for Illumina for Qiime. Similar workflow for mothur is available here.
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