Hi,
I have sequenced smallRNA sequences on Illumina HiSeq single end.
My reads are 100 nts, and at the 3'-end is the poly-a stretch from the oligo-dT adapter and sometimes also other nucleotides when the oligo-dT was sequenced through. But I do not understand where these come from (does not match the adapter it seems). Can someone suggest a good way to trim these reads from the poly-A stretch?
Sample seqs:
Adapters used:
Thanks!
I have sequenced smallRNA sequences on Illumina HiSeq single end.
My reads are 100 nts, and at the 3'-end is the poly-a stretch from the oligo-dT adapter and sometimes also other nucleotides when the oligo-dT was sequenced through. But I do not understand where these come from (does not match the adapter it seems). Can someone suggest a good way to trim these reads from the poly-A stretch?
Sample seqs:
Code:
@HWI-ST486:386:D1UMHACXX:3:1101:1399:2119 1:N:0:TGACCA NTCGTATCTGTAATCATGAACTTGTCAACGGCTACCTGGTTTCTGTCCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGAAGACCAAACTCTGGAACCCC + #1:BDBEDFHHGHGCBGHGCHHIJGIFGGIGEHCHJJIJHGH<FDGDHF@D@ACFEH6A>?BBB@>>B>BBB############################# @HWI-ST486:386:D1UMHACXX:3:1101:1367:2139 1:N:0:TGACCA NATGTTTTTTGGGGTTATAACAGGGTGGAGCGCTTTATGCGACTTCGCCCTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + #1=DDDEDHHDHHJJIGIFDFGIIJHGI?GHJIFHI@GG@F@;AH=?=BDCEE@@>@ABBDBBBD;BBBDDDDBB@BBDBBD@DBB>B@>>>5-59@<@BD @HWI-ST486:386:D1UMHACXX:3:1101:1392:2197 1:N:0:TGACCA ACAATTTATGGTAGAGAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGAAGAGCAAAGGTCTGAAACCCAGCCATTTACCATTCTCCTTTTCCCCTTTTTTT + CCCFFFFFHHHFFIIIIIIIIIFFGGGBBEDCBB=@#################################################################
Code:
TrueSeq_Sense_primer 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’ TrueSeq_Antisense_ NNNNNN_primer Barcode 5’-CAAGCAGAAGACGGCATACGAGAT-NNNNNN-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC(dT)25-3’