SmallRNA: how to trim poly-a stretch + other sequence at 5'-end?

[JonB]

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:

@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=@#################################################################

Adapters used:

TrueSeq_Sense_primer
5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’
TrueSeq_Antisense_ NNNNNN_primer Barcode
5’-CAAGCAGAAGACGGCATACGAGAT-NNNNNN-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC(dT)25-3’

Thanks!