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Old 12-01-2015, 05:07 AM   #1
Avidn
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Default Index sequences and alignment

Hi, i'm new to chip-seq analysis

I'm using bowtie in ordor to align the sequences from the fastq format. My question is do I have to remove the short index sequences (ilumina hi seq) or does bowtie knows how to deal with them?

Thx!
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Old 12-01-2015, 06:15 AM   #2
GenoMax
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With Illumina technology the index sequences (also called tag/barcode by some) are never a part of the actual sequence read.

That said, if you are referring to something else then please provide some clarification.
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Old 12-01-2015, 10:19 AM   #3
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Thx! that's exactly what I'm referring to.
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Old 12-01-2015, 10:27 AM   #4
GenoMax
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Long as your samples are demultiplexed (and in separate files) there is nothing more to do with barcodes.
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