I have a 51 single-end reads generated with MiSeq using NEBNext Multiplex Oligos for Illumina.
The sample sheet looks like this:
The Primer index manual can be found here.
Sor for HS130333-1 file, according to the manual above the primer/adapter with index is:
5 ́-CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3 ́
The document indicated that the expected index primer sequence read is TTAGGC which is the reverse complement of GCCTAA.
My question is if I use `trim_galore` or `cutadapt` to trim the data, what is the parameter -a I should use?
Is it the whole sequence above? Or first 5 ́-CAAGCAGAAGACGGCATACGAGAT?
Or GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3 ́? (and what is 's' means here)
Or the reverse complement of the each of above?
The sample sheet looks like this:
Code:
IEMFileVersion,4 Investigator Name,FB Experiment Name,WT10104 Date,11/27/2013 Workflow,GenerateFASTQ Application,FASTQ Only Assay,TruSeq Small RNA Description, Chemistry,Default [Reads] 51 [Settings] ReverseComplement,0 [Data] Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description HS130333-1,,,,RPI3,TTAGGC,, HS130333-2,,,,RPI4,TGACCA,, HS130333-3,,,,RPI5,ACAGTG,,
Sor for HS130333-1 file, according to the manual above the primer/adapter with index is:
5 ́-CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3 ́
The document indicated that the expected index primer sequence read is TTAGGC which is the reverse complement of GCCTAA.
My question is if I use `trim_galore` or `cutadapt` to trim the data, what is the parameter -a I should use?
Is it the whole sequence above? Or first 5 ́-CAAGCAGAAGACGGCATACGAGAT?
Or GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3 ́? (and what is 's' means here)
Or the reverse complement of the each of above?
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