Demultiplex Illumina With Barcodes On Sequence Read

Question

[rhasbunz]

Hi

I trying to use a public library of GBS in maize. The llumina reads have the bardcode included in sequences like this:

+SRR836350.1 HWI-ST1085:39:D0D7RACXX:2:1101:1270:1997 length=100
#4=DFFFFHHHHHJJJJJHHIIJJIJIJJJIJFHIIJJJJIJGIJJJJHIJJIJJIHHJJIGIJIJJIGHHFFFD?CECEEEEDDDDEDDDDDDDCCAC:
@SRR836350.2 HWI-ST1085:39:D0D7RACXX:2:1101:1383:1999 length=100
NTATTACTGCGCGCCGCGCTCGCCGCGGTGCATCCGGGGCTGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGC
+SRR836350.2 HWI-ST1085:39:D0D7RACXX:2:1101:1383:1999 length=100
#4=DFFFFHHFHHJJJJJJJJJJJJJHFEDDEEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBDBBDDDDDDDDDDDDDDDDDDCDD>
@SRR836350.3 HWI-ST1085:39:D0D7RACXX:2:1101:1981:1995 length=100
NGGCCAGCGAGCCTTTCTCTTCCTGCTACCACCCCACACCGCGCACACACCACCATCTCTCCTCGCCTCGCCTCCACTTCCTGGGCTACGTACCGGTCTC
+SRR836350.3 HWI-ST1085:39:D0D7RACXX:2:1101:1981:1995 length=100
#4=DFDFFHDFHHIJJIJJJJJJJIJJFHIIJJJJJIGIIJHIJIHGHFFFDDDDDCDDECCDDDDDDD5>BDDDDDCDDDDCCDDCADDDCDDDBDDDC
@SRR836350.4 HWI-ST1085:39:D0D7RACXX:2:1101:2049:1997 length=100
NTTGGATCAGCGACTGAGTCTCGCCGCGCTTTGCGATCTCGCCGAGCCAGTCGTTGACCCGCTTTAGCTGAGATCGGAAGAGCGGTTCAGCAGGAATGCC
+SRR836350.4 HWI-ST1085:39:D0D7RACXX:2:1101:2049:1997 length=100
#4=DDDFFHHHHHJJHIJHIJJJJJJIJJJJJJIJJJGHIGHHFDDDDADDDDD@AADDDDDDDDCDDDDDDCDDBD?BBDDDDDDDDDDDDDDDDDDDD
@SRR836350.5 HWI-ST1085:39:D0D7RACXX:2:1101:2090:2000 length=100
NAACGACAGCAACTGGCGCGTCGGTTGCTTGACGCGTGGGCCTGGGCTTCCAAGCTGTCGTGTCAGAAGTCGGAGAAGCGCGTCCACCTGGCGCGGCTGC
+SRR836350.5 HWI-ST1085:39:D0D7RACXX:2:1101:2090:2000 length=100
#4=DFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJJJHFFDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDB
@SRR836350.6 HWI-ST1085:39:D0D7RACXX:2:1101:3303:1994 length=100
NGTGTGGTCAGCTATCTCGTGCGTGCCGGGTACTGACAGGGAACAGCGAAACGATGGGTCCGACTCCGACGCCGGTCGCCCGGCCCCTGGACCCTCGCCG
+SRR836350.6 HWI-ST1085:39:D0D7RACXX:2:1101:3303:1994 length=100
#1=DDDFDHHHHHJJJJJJIJJJIJJJJJJDHIJJJJJIJJIJJJJJJJJHHFFFDDDADDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBDDDDDDDDB
@SRR836350.7 HWI-ST1085:39:D0D7RACXX:2:1101:3609:1992 length=100
NATCGTCTGTGACTTGAGCGGCAGGGACTGATTGTTCGGATGGCGTCTGTTCTGACATGGTCGTTCGATCAACAGTTTGATTGCTAGCATCAGGAGGCAG
+SRR836350.7 HWI-ST1085:39:D0D7RACXX:2:1101:3609:1992 length=100
#1=DFFDFHHFHHJJJJJJJJJJJJJEHIIGIIEFGGIJCHGIEHAEHEDEBCBDFEEEDAEDDDBDBDBBDDCDCADCCCDCCDDDCCDCDCDABDDDB
@SRR836350.8 HWI-ST1085:39:D0D7RACXX:2:1101:3586:1994 length=100
NTCAACAGCGAGGACGAACATAAGCCCCTGATGGGATTGCATGTGTCCGGCACATTGACATCGTCACAATTCATTCACATATAATATGCACACCACTGGC
+SRR836350.8 HWI-ST1085:39:D0D7RACXX:2:1101:3586:1994 length=100
#4=DDFFFHHHHHJJJJIJJJJJJIJJJJJIJJJJHJIJJIIJIJIJJJJHHFFFEEEEEEEDDDDDDCDDDDEDEDDDDDEEEDEEEDEDDDDDDCDDB
@SRR836350.9 HWI-ST1085:39:D0D7RACXX:2:1101:3681:1997 length=100
NGTGTGGTCTGCACTGGCCTGGATTGTGGACAGATCGATCCCCAAGAGCCCTAGGGTCTCGGCGTAGATGATGTTGGGGCTGAGATCGGAAGAGCGGTTC
+SRR836350.9 HWI-ST1085:39:D0D7RACXX:2:1101:3681:1997 length=100
#4=DDFFFHHGHHJJJJJJJJJIJJIHIJGIJIHIIJJJJJJJJJHGHIJJJJJJJFHIJJHHFBCD?DDCEDEDDDDDDDD8?@CDDDDDDABCDD@B?
@SRR836350.10 HWI-ST1085:39:D0D7RACXX:2:1101:3551:1998 length=100
NTCGATTCAGCCTCCGGCGCCCTGCTGGACGCAGGGGCGGCCTTCACAGACTTCGAACCGCCGGCGGCAGAGATCGGAAGAGCGGTTCAGCAGGAATGCC
+SRR836350.10 HWI-ST1085:39:D0D7RACXX:2:1101:3551:1998 length=100
#4=DFFFFHHHHHJJJJIJIJJJJJJJJJJJJJJJJJGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBDBBCCDADBBBBBCBD5>?DDDCDDBBADDC

How can to make demultiplexing of sequences?

Best

Rodrigo

Answer 1

[Ashutosh Pandey]

Try these tools:

1) Eautils

https://code.google.com/p/ea-utils/wiki/FastqMultx

2) Fastx

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_barcode_splitter_usage