I am a little confuse to the Flag of the BAM file from Bismark alignment. For the single-end data, everything is ok. Flag=0, or 16, in which 0 = 'Forward strand' while 16 = 'Reverse strand'.
However, for the paired-end data, it seems the situation is complicated. Do you know how to convert 99, 147, 83, 163 to 'Forward or Reverse strand'?
In my own opinion, 83 and 163 indicate 'Reverse strand' while 99 and 147 indicate "Forward strand" in bismark, right? However, actually in classic/traditional/conventional world,
99=64+32+2+1 = Forward (Up)
147=128+16+2+1 = Reverse (Bottom)
83= 64+16+2+1 = Reverse (Bottom)
163= 128+32+2+1 = Forward(Up)
19-08-2015: 0.14.4 released Bismark: Changed the FLAG values of paired-end alignments to the CTOT or CTOB strands so that reads can be properly displayed in SeqMonk when imported as BAM files. This change affects only paired-end alignments in --pbat or --non_directional mode. In detail we simply swapped the Read 1 and Read 2 FLAG values round so reads now resemble exactly concordant read pairs to the OT or OB strands. Note that results produced by the methylation extractor or further downstream of that are not affected by this change