I got a sequence data of PET to analysis. Read1 and Read2 have been already separated and put in two fastq file.
First I want to trim out the possible contaminated reads by Tagdust or Scythe.
I went to ask for the adapter sequences. I was told that they are N701 & N517, which is prepared with Illumina Nextera® Sample Preparation Kits. Then I search for the sequence and there is a table from Illumina:
i7 bases in adapter i7 index name i7 bases for entry on sample sheet TCGCCTTA N701 TAAGGCGA CTAGTACG N702 CGTACTAG TTCTGCCT N703 AGGCAGAA
Can anyone tell the difference of "i7 in adapter" and "i7 for entry on sample sheet"? Which one should I used for Tagdust? And the sequence of i7 should be the "barcode" parameter in Tagdust?
Here is about tagdust:
Thanks a lot for your help!