Tophat2 in strand-specific mode: discrepancy between 0x10 bit and XS flag

[Amelie]

Hi,

I've got single end RNA-seq reads coming from a strand-specific protocol. After running tophat2 v2.0.6 using the --library-type fr-firststrand option, how is it possible that I get reads with bit 0x10 not set and tag XS:A:- and reads with that bit set and the same tag XS:A:- ? I thought the value of the bit would specify the value of the flag, when tophat was run in strand-specific mode.

Any idea will be much appreciated.

Amelie

WTCHG_38037_194:6:1306:15231:88771#ATGAGATC 0 10 811101 50 96M2025N4M * 0 0 CTGCAGTTGGTCTTTAATGGCTTTTGTATGAGCCAGGTCATCCTCCAAGGCCGAGATCTGCCGGTAACCCTCTGAATGCTGCATTTCAAACTTCTCCTTC BCCFFFFFHHFHDIJJJIJIIJJJJJHIJJIJJJJIJGHIJJJJJJJJIIIJHIJIIIIJJJJHEBEECCEDECDDDDDC AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UU XS:A:- NH:i:1

WTCHG_38037_194:6:2308:7073:6272#ATGAGATC 16 10 811152 50 45M2025N55M * 0 0 CGAGATCTTCCGGTAACCCTCTGAATGCTGCATTTCAAACTTCTCCTTCACAGACTCCAGCTCCATTCGAAGGCGGTTATTCTCTGATAATAGGTCCCGG ##########@>@5556B@;5@>A>CA:>3B@DB:@?=.)? (C;9=8/8)4FC8BF=/?)2B>EF>DD<6GA@DCEBEF@?<:E4BGDDFCCABD?;@ AS:i:0 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:8G91 YT:Z:UU XS:A:- NH:i:1