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Old 02-26-2015, 03:07 PM   #189
Brian Bushnell
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Location: Walnut Creek, CA

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BBMap is a global aligner. If you use the local flag, it will trim global alignments to become local alignments, but it will not find terrible global alignments in the first place. When run at high sensitivity, this is the output:

Code:
@PG	ID:BBMap	PN:BBMap	VN:34.59	CL:java -Djava.library.path=/usr/common/jgi/utilities/bbtools/prod-v34.59/lib -ea -Xmx31g align2.BBMapPacBio build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambiguous=best minscaf=100 startpad=10000 stoppad=10000 midpad=6000 -Xmx31g t=1 k=11 in=pair3.fq out=pb.sam path=/global/projectb/sandbox/gaag/bbtools/hg191 reads=4 int=t ignorequality minratio=0.1 maxindel=40 vslow ambig=all customtag idtag ow reads=1
1 	99	chr1	40799086	4	3=3X2=3I4=40I46=	=	40799223	238	GAATTATAATCCCCATAATCTCCACCTGTCAAGGGTGGAACCAGATGTAGGTTATTTCCCTTGATGTCTACAATATCACCTTTCTTATAGATTCGCATATA	<<==<=<=>>==>=<===>>>===>=>=<=;>=>=<=>==>======<======>>=====>>=<==>>==<>====<====<>===<====<========	NM:i:46	AM:i:4	NH:i:2	YI:f:54.46	X1:Z:$1,0,40807085,40807142,0,00,32,3075,4058,6517,6517,,mmmSSSmmIIImmmmIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIImmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm$6,1,154470997,154471095,0,00,33,3754,4697,0,4697,,mSSSmmIIIImmImmSmmmIIIIIIIIIIIIIIImmmSmmSmmmmDDDDDDDDDDDDDDDDDDmmmmmmmmSmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm	X2:Z:m3S3mmI3m4I40m46	X3:i:4058	X4:i:101	X5:Z:0	X6:i:2054
1 	369	chr5	154462998	5	1=3X2=4I2=1I2=1X3=15I3=1X2=1X4=18D8=1X47=	chr1	40799223	0	*	*	NM:i:45	AM:i:5	NH:i:2	YI:f:62.18	X1:Z:$1,0,40807085,40807142,0,00,32,3075,4058,6517,6517,,mmmSSSmmIIImmmmIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIImmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm$6,1,154470997,154471095,0,00,33,3754,4697,0,4697,,mSSSmmIIIImmImmSmmmIIIIIIIIIIIIIIImmmSmmSmmmmDDDDDDDDDDDDDDDDDDmmmmmmmmSmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm	X2:Z:mS3mmI4mmImmSm3I15m3SmmSm4D18m8Sm47	X3:i:4697	X4:i:101	X5:Z:0	X6:i:34823
1 	147	chr1	40799223	44	101=	=	40799086	-238	TTTGTCATTTTGGCGAATTACTGGAAGGTGGCGTTTCTGGCCGTAAGGCTGATATTCTTCATTTTTAAACCCAATATAACCATCCTTTCCTGTAGACTCTT	========<<3===3===<333===<=====<====><==<========<======>>=>=>==><<=<=>>>==<=>=>=========><====<>====	NM:i:0	AM:i:40	NH:i:1	YI:f:100	X1:Z:$1,1,40807222,40807322,0,11,81,10090,10090,11079,11079,,mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm	X2:Z:m101	X3:i:10090	X4:i:101	X5:Z:0	X6:i:6159
The two alignments for the first read are at 62% and 54% identity, both of which are below what BBMap looks for at default settings.
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