Index sequences and alignment

[Avidn]

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!

[GenoMax]

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.

[Avidn]

Thx! that's exactly what I'm referring to.

[GenoMax]

Long as your samples are demultiplexed (and in separate files) there is nothing more to do with barcodes.