I have paired end fastq files but I can't figure out which option my file falls under -b, -b2, or -b4. Has anyone had experience doing this and can clarify how to determine which one my sequences are? The novoalign documentation isn't the clearest, the first few paragraphs here attempt to explain,
(http://www.novocraft.com/wiki/tiki-i...page_ref_id=21)
Here is the head of my fastq files:
R1:
@R0209721:283:C29BHACXX:3:1101:1693:1993/1
NGGGCGTGGTGGTATATGTTTGTAATTTTAGTTATTTGGGAGGTTGAGGTA
+
#1=DDDDDHCFHFHIJJJIIJJGIIJJJJGIFHGIJJJJJBHHFHIFHIFF
@R0209721:283:C29BHACXX:3:1101:1810:1989/1
NGGTGGAGATTATTGTATTTTATATGGATGGAGAGGTGACGGGTTTGTTTT
+
#1=BDFFFHHHHHJJGGIJJJJJJJJJJJJJIIGHH?HFHIJJDGIHFHIH
@R0209721:283:C29BHACXX:3:1101:3768:1988/1
NGGAATGGAATGGAATGTAATGGAATGGAATGGAATGGAATGGAATTAATT
R2:
@R0209721:283:C29BHACXX:3:1101:1693:1993/2
CAAATTCAAATAATTCTCCTACCTCAACCTCCCAAATAACTAAAATTACAA
+
CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJIIJIG
@R0209721:283:C29BHACXX:3:1101:1810:1989/2
CAAAAACAAACCCGTCACCTCTCCATCCATATAAAATACAATAATCTCCAC
+
CCCFFFFFHHHHHFBEGIJJJFHJIJJJJJJJIJJJJJJJJJJJJJIJJJF
@R0209721:283:C29BHACXX:3:1101:3768:1988/2
CAAAAAATTCCATTCCATTACATTCCATTCCAATCCATTCCCCTACACTCG
Much appreciated.
(http://www.novocraft.com/wiki/tiki-i...page_ref_id=21)
Here is the head of my fastq files:
R1:
@R0209721:283:C29BHACXX:3:1101:1693:1993/1
NGGGCGTGGTGGTATATGTTTGTAATTTTAGTTATTTGGGAGGTTGAGGTA
+
#1=DDDDDHCFHFHIJJJIIJJGIIJJJJGIFHGIJJJJJBHHFHIFHIFF
@R0209721:283:C29BHACXX:3:1101:1810:1989/1
NGGTGGAGATTATTGTATTTTATATGGATGGAGAGGTGACGGGTTTGTTTT
+
#1=BDFFFHHHHHJJGGIJJJJJJJJJJJJJIIGHH?HFHIJJDGIHFHIH
@R0209721:283:C29BHACXX:3:1101:3768:1988/1
NGGAATGGAATGGAATGTAATGGAATGGAATGGAATGGAATGGAATTAATT
R2:
@R0209721:283:C29BHACXX:3:1101:1693:1993/2
CAAATTCAAATAATTCTCCTACCTCAACCTCCCAAATAACTAAAATTACAA
+
CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJIIJIG
@R0209721:283:C29BHACXX:3:1101:1810:1989/2
CAAAAACAAACCCGTCACCTCTCCATCCATATAAAATACAATAATCTCCAC
+
CCCFFFFFHHHHHFBEGIJJJFHJIJJJJJJJIJJJJJJJJJJJJJIJJJF
@R0209721:283:C29BHACXX:3:1101:3768:1988/2
CAAAAAATTCCATTCCATTACATTCCATTCCAATCCATTCCCCTACACTCG
Much appreciated.