Hi all,
I am seeing this data from a paired end solexa run (pipeline 1.4). The sequence is identical, yet the identifiers (tile# on the flowcell, x and y coordinates) are different. In Bowtie alignment each sequence hits the same start and stop site.
First, is this PCR bias and second, should all the alignments be kept, none or only 1? Thank you for any comments.
@HWI-EAS261:6:2:675:1607#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
ACC=BBAC@CBB@B?;=BAC;?B4;@7BBAA@?;@>A@;=9<3;@
--
@HWI-EAS261:6:7:1000:1185#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
BCCBCCBCBBBCBCACABCABCBBABCBCCBB@B@BBB9B@A@=6
--
@HWI-EAS261:6:22:934:1507#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
BC>ABBCBABCBCCCCC>BBABBCCBCBCCBB@BBB8B@A@@;<;
--
@HWI-EAS261:6:24:285:958#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
BBB7BBA@B@@@?@A?AB@AAB@B@B@A?B@@=?8@=<<7;<<?7
--
@HWI-EAS261:6:60:421:1920#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
BCB?;CBCCBBB;BA@BCBBBAABBBCCBB?B;;<9@:1)5<=@@
--
@HWI-EAS261:6:72:284:58#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
<<A<ACCCCCACCBBCCCBAA<ACBBCBACBB>A<A6@>A@><76
Layla
I am seeing this data from a paired end solexa run (pipeline 1.4). The sequence is identical, yet the identifiers (tile# on the flowcell, x and y coordinates) are different. In Bowtie alignment each sequence hits the same start and stop site.
First, is this PCR bias and second, should all the alignments be kept, none or only 1? Thank you for any comments.
@HWI-EAS261:6:2:675:1607#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
ACC=BBAC@CBB@B?;=BAC;?B4;@7BBAA@?;@>A@;=9<3;@
--
@HWI-EAS261:6:7:1000:1185#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
BCCBCCBCBBBCBCACABCABCBBABCBCCBB@B@BBB9B@A@=6
--
@HWI-EAS261:6:22:934:1507#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
BC>ABBCBABCBCCCCC>BBABBCCBCBCCBB@BBB8B@A@@;<;
--
@HWI-EAS261:6:24:285:958#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
BBB7BBA@B@@@?@A?AB@AAB@B@B@A?B@@=?8@=<<7;<<?7
--
@HWI-EAS261:6:60:421:1920#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
BCB?;CBCCBBB;BA@BCBBBAABBBCCBB?B;;<9@:1)5<=@@
--
@HWI-EAS261:6:72:284:58#0/1
ATGTGCTCACCTGCCTCATCCATACACATACGTGGCTGCTCTCAC
+
<<A<ACCCCCACCBBCCCBAA<ACBBCBACBB>A<A6@>A@><76
Layla
Comment