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Old 01-26-2014, 10:30 PM   #1
foolishbrat
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Posts: 44
Default Best way to trim MiSeq - NEBNext Multiplex Oligos for Illumina Library

I have a 51 single-end reads generated with MiSeq using NEBNext Multiplex Oligos for Illumina.

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,,
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?

Last edited by foolishbrat; 01-26-2014 at 10:33 PM.
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Old 01-27-2014, 04:10 AM   #2
GenoMax
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Cross-posted and solved: http://seqanswers.com/forums/showthread.php?t=40290
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adapter, bioinformatics, primer, trim

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