The following is the head for one of my paired fastq file:
@HWI-M04771:60:000000000-AURUP:1:1101:15803:1815 1:N:0:TGAGGTTTGATG TACGGGGGATGCAAGCGTTATCCGGAATCATTGGGCGTAAAGCGCCTGTAGGTTGTTTAGTAAGTCCATTGTTAAAGACCAGGGCTTAACCCTGGGAAAGCAATAGAAACTACTAGACTTGAGTATGGCAGGGGTAGAGGGAATTTCTAGTGTAGCGGTGAAATGCGTAGATATTAGAAAGAACACCGGTGGCGAAAGCGCTCTACTGGACCATTACTGACACTGAGAGGCGAAAGCTAGGGTAGCAAAAGGG + BBBBBBFBBBFFEGGCEFGAGAGGGFFF3CAGFGGGHHGGFHFACEEGGGGGEGFEGFHDGHHGHFF<BGHGHHHH>BCCGCCHHFFGGFEEGFC2HGDFEG3FDGG@FGGDGGHFGFGDHHGHFDF?<GHFFHFGFFFDHHGHHHHHGCGHHHGHHHGHHHEGE=DFHHHHHHHHHHHHHEE0EFEAA@DEEHFECEFA?ADBHGGGGGB;BFFHGFEFGFHHGHEEECGGGGGGFFGGGFFFFFFFB>3>>
Since the index sequence is present in the first line, does that imply I need to process it and match it with a separate barcode fastq file using split_libraries_fast.py. I haven't received a barcode file as such from the sequencing lab and want confirm if I need to have that.
Do I have to include it in my mapping file?
Any help is appreciated a lot!