I went to dump some ChIP-seq reads to a BED file using sam2bed, and found
that they all had a strand of '*'.  Looking into it a bit further, the
culprit seemed to be the alignments written to the SAM file, e.g.

H9_WYSOCKA_NEURAL.H3K27ac.643   4       *       0       0       *
chr1    1       0       GGTAGGCGGAGCTTGCAGTGAGCTGAGATCGCGCCA
 AA>5A=CA745A%%%%%%%%%%%%%%%%%%%%%%%%
H9_WYSOCKA_NEURAL.H3K27ac.644   16      chr3    54404886        199     36M
    *       0       0       CACTTTAACATTTTTCCTTCAATCTCAGCATTCCTC
C>C=@5:@==4=A?=CDBDDD=-D:DCCEECADD5B
   AS:i:5  NM:i:0
H9_WYSOCKA_NEURAL.H3K27ac.645   0       chr17   7073894 199     36M     *
    0       0       GTAAACTTGTCTGTTTTCTTATACCTCTAAAATTTT    D5?DDC=ABA:@
:=@BCBB8:B=?BBBDBB?:>5@B    AS:i:6  NM:i:0
H9_WYSOCKA_NEURAL.H3K27ac.646   4       *       0       0       *
chr1    1       0       CAGAGGACGGTACCTGTATTAAATGTATTAGACAGG
 3?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
H9_WYSOCKA_NEURAL.H3K27ac.647   4       *       0       0       *
chr1    1       0       GTCCCAACCAGAGGCCCTGAGCGGAGGTTCTCGGGG
 ;7,4>,B<=6C>C:?%%%%%%%%%%%%%%%%%%%%%
H9_WYSOCKA_NEURAL.H3K27ac.648   4       *       0       0       *
chr1    1       0       ATATTGACAACTGCCGGCAATTGGCATCATCTATCT
 ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
H9_WYSOCKA_NEURAL.H3K27ac.649   4       *       0       0       *
chr1    1       0       TGCATTCTTTTGGAGGAGGAGAGGTGCTCTGCTTTT
 ADC=ED-=D;=@C5CD,DA4D:DDADBB5?D:D:5>

Previously, I didn't have this problem (I went back and checked).  So
despite my worries that sam2bed was somehow to blame, it was just doing
what it was told (although I would like it if proper BED6 output was the
default from sam2bed!).  This seems to be an alignment issue.

Do I need to rebuild my indices for R-3.0/Rsubread 1.10 or some such?

Here is what I'm running:

Welcome to R version 3.0.0 (2013-04-03)
> packageVersion('Rsubread')
[1] ‘1.10.1’

-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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