[GenoMax]

Looks like this (T's changed to U's): http://www.ncbi.nlm.nih.gov/nuccore/9629357/

[lankage]

>NC_001802DRannotations_(modified)
GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAAUAAAGCUUGCCUUGAGUGCUUCAAGUAGUGUGUGCCCGUCUGUUGUGUGACUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGGGAAACCAGAGGAGCUCUCUCGACGCAGGACUCGGCUUGCUGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACUGGUGAGUACGCCAAAAAUUUUGACUAGCGGAGGCUAGAAGGAGAGAGAUGGGUGCGAGAGCGUCAGUAUUAAGCGGGGGAGAAUUAGAUCGAUGGGAAAAAAUUCGGUUAAGGCCAGGGGGAAAGAAAAAAUAUAAAUUAAAACAUAUAGUAUGGGCAAGCAGGGAGCUAGAACGAUUCGCAGUUAAUCCUGGCCUGUUAGAAACAUCAGAAGGCUGUAGACAAAUACUGGGACAGCUACAACCAUCCCUUCAGACAGGAUCAGAAGAACUUAGAUCAUUAUAUAAUACAGUAGCAACCCUCUAUUGUGUGCAUCAAAGGAUAGAGAUAAAAGACACCAAGGAAGCUUUAGACAAGAUAGAGGAAGAGCAAAACAAAAGUAAGAAAAAAGCACAGCAAGCAGCAGCUGACACAGGACACAGCAAUCAGGUCAGCCAAAAUUACCCUAUAGUGCAGAACAUCCAGGGGCAAAUGGUACAUCAGGCCAUAUCACCUAGAACUUUAAAUGCAUGGGUAAAAGUAGUAGAAGAGAAGGCUUUCAGCCCAGAAGUGAUACCCAUGUUUUCAGCAUUAUCAGAAGGAGCCACCCCACAAGAUUUAAACACCAUGCUAAACACAGUGGGGGGACAUCAAGCAGCCAUGCAAAUGUUAAAAGAGACCAUCAAUGAGGAAGCUGCAGAAUGGGAUAGAGUGCAUCCAGUGCAUGCAGGGCCUAUUGCACCAGGCCAGAUGAGAGAACCAAGGGGAAGUGACAUAGCAGGAACUACUAGUACCCUUCAGGAACAAAUAGGAUGGAUGACAAAUAAUCCACCUAUCCCAGUAGGAGAAAUUUAUAAAAGAUGGAUAAUCCUGGGAUUAAAUAAAAUAGUAAGAAUGUAUAGCCCUACCAGCAUUCUGGACAUAAGACAAGGACCAAAGGAACCCUUUAGAGACUAUGUAGACCGGUUCUAUAAAACUCUAAGAGCCGAGCAAGCUUCACAGGAGGUAAAAAAUUGGAUGACAGAAACCUUGUUGGUCCAAAAUGCGAACCCAGAUUGUAAGACUAUUUUAAAAGCAUUGGGACCAGCGGCUACACUAGAAGAAAUGAUGACAGCAUGUCAGGGAGUAGGAGGACCCGGCCAUAAGGCAAGAGUUUUGGCUGAAGCAAUGAGCCAAGUAACAAAUUCAGCUACCAUAAUGAUGCAGAGAGGCAAUUUUAGGAACCAAAGAAAGAUUGUUAAGUGUUUCAAUUGUGGCAAAGAAGGGCACACAGCCAGAAAUUGCAGGGCCCCUAGGAAAAAGGGCUGUUGGAAAUGUGGAAAGGAAGGACACCAAAUGAAAGAUUGUACUGAGAGACAGGCUAAUUUUUUAGGGAAGAUCUGGCCUUCCUACAAGGGAAGGCCAGGGAAUUUUCUUCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCUUCAGGUCUGGGGUAGAGACAACAACUCCCCCUCAGAAGCAGGAGCCGAUAGACAAGGAACUGUAUCCUUUAACUUCCCUCAGGUCACUCUUUGGCAACGACCCCUCGUCACAAUAAAGAUAGGGGGGCAACUAAAGGAAGCUCUAUUAGAUACAGGAGCAGAUGAUACAGUAUUAGAAGAAAUGAGUUUGCCAGGAAGAUGGAAACCAAAAAUGAUAGGGGGAAUUGGAGGUUUUAUCAAAGUAAGACAGUAUGAUCAGAUACUCAUAGAAAUCUGUGGACAUAAAGCUAUAGGUACAGUAUUAGUAGGACCUACACCUGUCAACAUAAUUGGAAGAAAUCUGUUGACUCAGAUUGGUUGCACUUUAAAUUUUCCCAUUAGCCCUAUUGAGACUGUACCAGUAAAAUUAAAGCCAGGAAUGGAUGGCCCAAAAGUUAAACAAUGGCCAUUGACAGAAGAAAAAAUAAAAGCAUUAGUAGAAAUUUGUACAGAGAUGGAAAAGGAAGGGAAAAUUUCAAAAAUUGGGCCUGAAAAUCCAUACAAUACUCCAGUAUUUGCCAUAAAGAAAAAAGACAGUACUAAAUGGAGAAAAUUAGUAGAUUUCAGAGAACUUAAUAAGAGAACUCAAGACUUCUGGGAAGUUCAAUUAGGAAUACCACAUCCCGCAGGGUUAAAAAAGAAAAAAUCAGUAACAGUACUGGAUGUGGGUGAUGCAUAUUUUUCAGUUCCCUUAGAUGAAGACUUCAGGAAGUAUACUGCAUUUACCAUACCUAGUAUAAACAAUGAGACACCAGGGAUUAGAUAUCAGUACAAUGUGCUUCCACAGGGAUGGAAAGGAUCACCAGCAAUAUUCCAAAGUAGCAUGACAAAAAUCUUAGAGCCUUUUAGAAAACAAAAUCCAGACAUAGUUAUCUAUCAAUACAUGGAUGAUUUGUAUGUAGGAUCUGACUUAGAAAUAGGGCAGCAUAGAACAAAAAUAGAGGAGCUGAGACAACAUCUGUUGAGGUGGGGACUUACCACACCAGACAAAAAACAUCAGAAAGAACCUCCAUUCCUUUGGAUGGGUUAUGAACUCCAUCCUGAUAAAUGGACAGUACAGCCUAUAGUGCUGCCAGAAAAAGACAGCUGGACUGUCAAUGACAUACAGAAGUUAGUGGGGAAAUUGAAUUGGGCAAGUCAGAUUUACCCAGGGAUUAAAGUAAGGCAAUUAUGUAAACUCCUUAGAGGAACCAAAGCACUAACAGAAGUAAUACCACUAACAGAAGAAGCAGAGCUAGAACUGGCAGAAAACAGAGAGAUUCUAAAAGAACCAGUACAUGGAGUGUAUUAUGACCCAUCAAAAGACUUAAUAGCAGAAAUACAGAAGCAGGGGCAAGGCCAAUGGACAUAUCAAAUUUAUCAAGAGCCAUUUAAAAAUCUGAAAACAGGAAAAUAUGCAAGAAUGAGGGGUGCCCACACUAAUGAUGUAAAACAAUUAACAGAGGCAGUGCAAAAAAUAACCACAGAAAGCAUAGUAAUAUGGGGAAAGACUCCUAAAUUUAAACUGCCCAUACAAAAGGAAACAUGGGAAACAUGGUGGACAGAGUAUUGGCAAGCCACCUGGAUUCCUGAGUGGGAGUUUGUUAAUACCCCUCCCUUAGUGAAAUUAUGGUACCAGUUAGAGAAAGAACCCAUAGUAGGAGCAGAAACCUUCUAUGUAGAUGGGGCAGCUAACAGGGAGACUAAAUUAGGAAAAGCAGGAUAUGUUACUAAUAGAGGAAGACAAAAAGUUGUCACCCUAACUGACACAACAAAUCAGAAGACUGAGUUACAAGCAAUUUAUCUAGCUUUGCAGGAUUCGGGAUUAGAAGUAAACAUAGUAACAGACUCACAAUAUGCAUUAGGAAUCAUUCAAGCACAACCAGAUCAAAGUGAAUCAGAGUUAGUCAAUCAAAUAAUAGAGCAGUUAAUAAAAAAGGAAAAGGUCUAUCUGGCAUGGGUACCAGCACACAAAGGAAUUGGAGGAAAUGAACAAGUAGAUAAAUUAGUCAGUGCUGGAAUCAGGAAAGUACUAUUUUUAGAUGGAAUAGAUAAGGCCCAAGAUGAACAUGAGAAAUAUCACAGUAAUUGGAGAGCAAUGGCUAGUGAUUUUAACCUGCCACCUGUAGUAGCAAAAGAAAUAGUAGCCAGCUGUGAUAAAUGUCAGCUAAAAGGAGAAGCCAUGCAUGGACAAGUAGACUGUAGUCCAGGAAUAUGGCAACUAGAUUGUACACAUUUAGAAGGAAAAGUUAUCCUGGUAGCAGUUCAUGUAGCCAGUGGAUAUAUAGAAGCAGAAGUUAUUCCAGCAGAAACAGGGCAGGAAACAGCAUAUUUUCUUUUAAAAUUAGCAGGAAGAUGGCCAGUAAAAACAAUACAUACUGACAAUGGCAGCAAUUUCACCGGUGCUACGGUUAGGGCCGCCUGUUGGUGGGCGGGAAUCAAGCAGGAAUUUGGAAUUCCCUACAAUCCCCAAAGUCAAGGAGUAGUAGAAUCUAUGAAUAAAGAAUUAAAGAAAAUUAUAGGACAGGUAAGAGAUCAGGCUGAACAUCUUAAGACAGCAGUACAAAUGGCAGUAUUCAUCCACAAUUUUAAAAGAAAAGGGGGGAUUGGGGGGUACAGUGCAGGGGAAAGAAUAGUAGACAUAAUAGCAACAGACAUACAAACUAAAGAAUUACAAAAACAAAUUACAAAAAUUCAAAAUUUUCGGGUUUAUUACAGGGACAGCAGAAAUCCACUUUGGAAAGGACCAGCAAAGCUCCUCUGGAAAGGUGAAGGGGCAGUAGUAAUACAAGAUAAUAGUGACAUAAAAGUAGUGCCAAGAAGAAAAGCAAAGAUCAUUAGGGAUUAUGGAAAACAGAUGGCAGGUGAUGAUUGUGUGGCAAGUAGACAGGAUGAGGAUUAGAACAUGGAAAAGUUUAGUAAAACACCAUAUGUAUGUUUCAGGGAAAGCUAGGGGAUGGUUUUAUAGACAUCACUAUGAAAGCCCUCAUCCAAGAAUAAGUUCAGAAGUACACAUCCCACUAGGGGAUGCUAGAUUGGUAAUAACAACAUAUUGGGGUCUGCAUACAGGAGAAAGAGACUGGCAUUUGGGUCAGGGAGUCUCCAUAGAAUGGAGGAAAAAGAGAUAUAGCACACAAGUAGACCCUGAACUAGCAGACCAACUAAUUCAUCUGUAUUACUUUGACUGUUUUUCAGACUCUGCUAUAAGAAAGGCCUUAUUAGGACACAUAGUUAGCCCUAGGUGUGAAUAUCAAGCAGGACAUAACAAGGUAGGAUCUCUACAAUACUUGGCACUAGCAGCAUUAAUAACACCAAAAAAGAUAAAGCCACCUUUGCCUAGUGUUACGAAACUGACAGAGGAUAGAUGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAAUGAAUGGACACUAGAGCUUUUAGAGGAGCUUAAGAAUGAAGCUGUUAGACAUUUUCCUAGGAUUUGGCUCCAUGGCUUAGGGCAACAUAUCUAUGAAACUUAUGGGGAUACUUGGGCAGGAGUGGAAGCCAUAAUAAGAAUUCUGCAACAACUGCUGUUUAUCCAUUUUCAGAAUUGGGUGUCGACAUAGCAGAAUAGGCGUUACUCGACAGAGGAGAGCAAGAAAUGGAGCCAGUAGAUCCUAGACUAGAGCCCUGGAAGCAUCCAGGAAGUCAGCCUAAAACUGCUUGUACCAAUUGCUAUUGUAAAAAGUGUUGCUUUCAUUGCCAAGUUUGUUUCAUAACAAAAGCCUUAGGCAUCUCCUAUGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCUCAUCAGAACAGUCAGACUCAUCAAGCUUCUCUAUCAAAGCAGUAAGUAGUACAUGUAAUGCAACCUAUACCAAUAGUAGCAAUAGUAGCAUUAGUAGUAGCAAUAAUAAUAGCAAUAGUUGUGUGGUCCAUAGUAAUCAUAGAAUAUAGGAAAAUAUUAAGACAAAGAAAAAUAGACAGGUUAAUUGAUAGACUAAUAGAAAGAGCAGAAGACAGUGGCAAUGAGAGUGAAGGAGAAAUAUCAGCACUUGUGGAGAUGGGGGUGGAGAUGGGGCACCAUGCUCCUUGGGAUGUUGAUGAUCUGUAGUGCUACAGAAAAAUUGUGGGUCACAGUCUAUUAUGGGGUACCUGUGUGGAAGGAAGCAACCACCACUCUAUUUUGUGCAUCAGAUGCUAAAGCAUAUGAUACAGAGGUACAUAAUGUUUGGGCCACACAUGCCUGUGUACCCACAGACCCCAACCCACAAGAAGUAGUAUUGGUAAAUGUGACAGAAAAUUUUAACAUGUGGAAAAAUGACAUGGUAGAACAGAUGCAUGAGGAUAUAAUCAGUUUAUGGGAUCAAAGCCUAAAGCCAUGUGUAAAAUUAACCCCACUCUGUGUUAGUUUAAAGUGCACUGAUUUGAAGAAUGAUACUAAUACCAAUAGUAGUAGCGGGAGAAUGAUAAUGGAGAAAGGAGAGAUAAAAAACUGCUCUUUCAAUAUCAGCACAAGCAUAAGAGGUAAGGUGCAGAAAGAAUAUGCAUUUUUUUAUAAACUUGAUAUAAUACCAAUAGAUAAUGAUACUACCAGCUAUAAGUUGACAAGUUGUAACACCUCAGUCAUUACACAGGCCUGUCCAAAGGUAUCCUUUGAGCCAAUUCCCAUACAUUAUUGUGCCCCGGCUGGUUUUGCGAUUCUAAAAUGUAAUAAUAAGACGUUCAAUGGAACAGGACCAUGUACAAAUGUCAGCACAGUACAAUGUACACAUGGAAUUAGGCCAGUAGUAUCAACUCAACUGCUGUUAAAUGGCAGUCUAGCAGAAGAAGAGGUAGUAAUUAGAUCUGUCAAUUUCACGGACAAUGCUAAAACCAUAAUAGUACAGCUGAACACAUCUGUAGAAAUUAAUUGUACAAGACCCAACAACAAUACAAGAAAAAGAAUCCGUAUCCAGAGAGGACCAGGGAGAGCAUUUGUUACAAUAGGAAAAAUAGGAAAUAUGAGACAAGCACAUUGUAACAUUAGUAGAGCAAAAUGGAAUAACACUUUAAAACAGAUAGCUAGCAAAUUAAGAGAACAAUUUGGAAAUAAUAAAACAAUAAUCUUUAAGCAAUCCUCAGGAGGGGACCCAGAAAUUGUAACGCACAGUUUUAAUUGUGGAGGGGAAUUUUUCUACUGUAAUUCAACACAACUGUUUAAUAGUACUUGGUUUAAUAGUACUUGGAGUACUGAAGGGUCAAAUAACACUGAAGGAAGUGACACAAUCACCCUCCCAUGCAGAAUAAAACAAAUUAUAAACAUGUGGCAGAAAGUAGGAAAAGCAAUGUAUGCCCCUCCCAUCAGUGGACAAAUUAGAUGUUCAUCAAAUAUUACAGGGCUGCUAUUAACAAGAGAUGGUGGUAAUAGCAACAAUGAGUCCGAGAUCUUCAGACCUGGAGGAGGAGAUAUGAGGGACAAUUGGAGAAGUGAAUUAUAUAAAUAUAAAGUAGUAAAAAUUGAACCAUUAGGAGUAGCACCCACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGAAUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCCUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGAAUGCUAGUUGGAGUAAUAAAUCUCUGGAACAGAUUUGGAAUCACACGACCUGGAUGGAGUGGGACAGAGAAAUUAACAAUUACACAAGCUUAAUACACUCCUUAAUUGAAGAAUCGCAAAACCAGCAAGAAAAGAAUGAACAAGAAUUAUUGGAAUUAGAUAAAUGGGCAAGUUUGUGGAAUUGGUUUAACAUAACAAAUUGGCUGUGGUAUAUAAAAUUAUUCAUAAUGAUAGUAGGAGGCUUGGUAGGUUUAAGAAUAGUUUUUGCUGUACUUUCUAUAGUGAAUAGAGUUAGGCAGGGAUAUUCACCAUUAUCGUUUCAGACCCACCUCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAAUAGAAGAAGAAGGUGGAGAGAGAGACAGAGACAGAUCCAUUCGAUUAGUGAACGGAUCCUUGGCACUUAUCUGGGACGAUCUGCGGAGCCUGUGCCUCUUCAGCUACCACCGCUUGAGAGACUUACUCUUGAUUGUAACGAGGAUUGUGGAACUUCUGGGACGCAGGGGGUGGGAAGCCCUCAAAUAUUGGUGGAAUCUCCUACAGUAUUGGAGUCAGGAACUAAAGAAUAGUGCUGUUAGCUUGCUCAAUGCCACAGCCAUAGCAGUAGCUGAGGGGACAGAUAGGGUUAUAGAAGUAGUACAAGGAGCUUGUAGAGCUAUUCGCCACAUACCUAGAAGAAUAAGACAGGGCUUGGAAAGGAUUUUGCUAUAAGAUGGGUGGCAAGUGGUCAAAAAGUAGUGUGAUUGGAUGGCCUACUGUAAGGGAAAGAAUGAGACGAGCUGAGCCAGCAGCAGAUAGGGUGGGAGCAGCAUCUCGAGACCUGGAAAAACAUGGAGCAAUCACAAGUAGCAAUACAGCAGCUACCAAUGCUGCUUGUGCCUGGCUAGAAGCACAAGAGGAGGAGGAGGUGGGUUUUCCAGUCACACCUCAGGUACCUUUAAGACCAAUGACUUACAAGGCAGCUGUAGAUCUUAGCCACUUUUUAAAAGAAAAGGGGGGACUGGAAGGGCUAAUUCACUCCCAAAGAAGACAAGAUAUCCUUGAUCUGUGGAUCUACCACACACAAGGCUACUUCCCUGAUUAGCAGAACUACACACCAGGGCCAGGGGUCAGAUAUCCACUGACCUUUGGAUGGUGCUACAAGCUAGUACCAGUUGAGCCAGAUAAGAUAGAAGAGGCCAAUAAAGGAGAGAACACCAGCUUGUUACACCCUGUGAGCCUGCAUGGGAUGGAUGACCCGGAGAGAGAAGUGUUAGAGUGGAGGUUUGACAGCCGCCUAGCAUUUCAUCACGUGGCCCGAGAGCUGCAUCCGGAGUACUUCAAGAACUGCUGACAUCGAGCUUGCUACAAGGGACUUUCCGCUGGGGACUUUCCAGGGAGGCGUGGCCUGGGCGGGACUGGGGAGUGGCGAGCCCUCAGAUCCUGCAUAUAAGCAGCUGCUUUUUGCCUGUACUGGGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAAUAAAGCUUGCCUUGAGUGCUUC

[Brian Bushnell]

That should not happen... outm should only print mapped reads, except when processing paired data, in which case it will print unmapped reads if the mate is mapped. But according to the flag you are processing single-ended data and that read was mapped, so it should have a cigar string.

It's possible that this is a bug that I've fixed since v34.92, but I have no record of that in my changelog. So I'd like to try to replicate it to see if it's a current bug. I already have the read, but can you send me or direct me to the specific reference you are using?

Thanks,
Brian

[lankage]

Hi Brian,
Came across an instance today where I was attempting to parse bbmap SAM output for cigar string information to observe the mapping of some HIV read sequences against a reference. I was expecting for a cigar string to be present for each record when using the outm=output.sam parameter. In one of my mapping records, I observed an asterisk instead. Am I wrong to assume outm= is intended to include only those mapped reads? I can filter out these reads, but I'd like to make sure my mapping parameters make sense.

From the SAM output:
@HD VN:1.4 SO:unsorted
@SQ SN:NC_001802DRannotations_(modified) LN:9181
@PG ID:BBMap PN:BBMap VN:34.92 CL:java -Djava.library.path=/home/dnanexus/bbmap/jni/ -ea -Xmx10g align2.BBMap build=1 overwrite=true fastareadlen=500 in=reads_file ref=ref_file outm=sam_output minid=.8 strictmaxindel=10 k=8 subfilter=15 -Xmx10g

The offending mapping record:
M01472:214:000000000-AG0YC:1:2108:10755:20410 1:N:0:78 0 NC_001802DRannotations_(modified) 2154 4 * * 0 0 AAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTCATAGTAATATGGGGAAAGACTCCTAAATTTAAATTACCCATACAAAAGGAAACATGGGAAGCATGGTGGACAGAGTATTGGC CCCCCGGGGGGGGGGGGGGGGGGGGGGFDCFGECGGGF<AFEGGFEFGGGGFGGGGGGGGGGGGGGGGGFGFFGGFGEFGGAGFGEAFF<,FGGGGGGGGGGFGGFDGGGFECFGGGGGGGGGGCCCCC AM:i:4

This only occurred after parsing ~8 million mapping records out of a total 50 million.

[Brian Bushnell]

You can change gap penalties and get a different alignment by adding the flag "msa=MultiStateAligner9Flat". That will generally reduce the rate of long indels by flattening the affine transforms. The resulting cigar string is "2=1D1X1=1X3=2X1=2X2=3I4=1I1X1=3I3=1X5=1X23=1X27=1X82=", which may not be exactly what you are looking for, but is much closer.

Alternatively, depending on what you are doing with the data, you can enable soft-clipping with BBMap's "local" flag, then calculate coverage using pileup.sh with the "includesoftclip" flag. This will calculate coverage including soft-clipped sequences.

Please let me know if neither of those is adequate...