Hi,
I understand that Bowtie offers the 'maxbts' and 'pairtries' parameters to control the trade-off between processing time and comprehensive search.
The following scenario is confusing me: if I map both ends of an ambiguous pair to hg19 independently, setting maxbts to 10billion, I get back 12k hits for end #1 and 14k hits for end #2.
However, if I map the pair as a pair, using 'tryhard' to give a high 'pairtries', I end up getting back pairings where one of the ends maps to a location that wasn't picked up in the original independent search.
My question is: what would cause the independent search to miss matches that the paired search picks up? I presumed that memory and maxbts are the only limiting factors?
Thanks,
Bio.X2Y
Inputs:
File: dodgy_input_1
@HWI-EAS283:2:1:810:1386#0/1
GGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCTG
+HWI-EAS283:2:1:810:1386#0/1
]bZ``aaabbbbb`bX`_babbaa`abb`aaaaaa``aaa
File: dodgy_input_2
@HWI-EAS283:2:1:810:1386#0/2
CCCGGGTTCAACCAATTCTCCTGCCTCAGCCTCCTGAGTA
+HWI-EAS283:2:1:810:1386#0/2
a_a_Zbababaa`bbbbababb`babbb]_aaaabbabab
Independent Search:
time /Volumes/Thymine/bowtie-0.12.5/bowtie \
-t \
-n 2 \
-m 100000 \
-a \
-p 4 \
--maxbts 1000000000 \
--best \
--solexa1.3-quals \
--chunkmbs 128 \
hg19 \
dodgy_input_1,dodgy_input_2 \
--un dodgy_pair_independent_unmatched.bowtie \
--max dodgy_pair_independent_ambiguous.bowtie \
dodgy_pair_independent_matched.bowtie \
&> dodgy_pair_independent_console.out
Paired Search:
time /Volumes/Thymine/bowtie-0.12.5/bowtie \
-t \
-n 2 \
-m 1000 \
-a \
-p 4 \
--best \
--tryhard \
--solexa1.3-quals \
--chunkmbs 128 \
hg19 \
-1 dodgy_input_1 \
-2 dodgy_input_2 \
--un dodgy_pair_pe_unmatched.bowtie \
--max dodgy_pair_pe_ambiguous.bowtie \
dodgy_pair_pe_matched.bowtie \
&> dodgy_pair_pe_console.out
Results:
For the independent search, I get 12,637 matches to end #1 and 13,946 matches to end #2.
For the paired search, I get 919 pairs (although I expected 393 since that many pair combinations from the original results can be combined to form pairs that satisfy -I and -X).
Example of result pair that has a mapping for end #2 that did not appear in the independent search:
HWI-EAS283:2:1:810:1386#0/1 + chr11 107533126 GGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCTG >C;AABBBCCCCCAC9A@CBCCBBABCCABBBBBBAABBB 344
HWI-EAS283:2:1:810:1386#0/2 - chr11 107533223 TACTCAGGAGGCTGAGGCAGGAGAATTGGTTGAACCCGGG CBCBCCBBBB@>CCCBCACCBCBCCCCABBCBCBC;@B@B 344 11:C>G,13:C>T
I understand that Bowtie offers the 'maxbts' and 'pairtries' parameters to control the trade-off between processing time and comprehensive search.
The following scenario is confusing me: if I map both ends of an ambiguous pair to hg19 independently, setting maxbts to 10billion, I get back 12k hits for end #1 and 14k hits for end #2.
However, if I map the pair as a pair, using 'tryhard' to give a high 'pairtries', I end up getting back pairings where one of the ends maps to a location that wasn't picked up in the original independent search.
My question is: what would cause the independent search to miss matches that the paired search picks up? I presumed that memory and maxbts are the only limiting factors?
Thanks,
Bio.X2Y
Inputs:
File: dodgy_input_1
@HWI-EAS283:2:1:810:1386#0/1
GGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCTG
+HWI-EAS283:2:1:810:1386#0/1
]bZ``aaabbbbb`bX`_babbaa`abb`aaaaaa``aaa
File: dodgy_input_2
@HWI-EAS283:2:1:810:1386#0/2
CCCGGGTTCAACCAATTCTCCTGCCTCAGCCTCCTGAGTA
+HWI-EAS283:2:1:810:1386#0/2
a_a_Zbababaa`bbbbababb`babbb]_aaaabbabab
Independent Search:
time /Volumes/Thymine/bowtie-0.12.5/bowtie \
-t \
-n 2 \
-m 100000 \
-a \
-p 4 \
--maxbts 1000000000 \
--best \
--solexa1.3-quals \
--chunkmbs 128 \
hg19 \
dodgy_input_1,dodgy_input_2 \
--un dodgy_pair_independent_unmatched.bowtie \
--max dodgy_pair_independent_ambiguous.bowtie \
dodgy_pair_independent_matched.bowtie \
&> dodgy_pair_independent_console.out
Paired Search:
time /Volumes/Thymine/bowtie-0.12.5/bowtie \
-t \
-n 2 \
-m 1000 \
-a \
-p 4 \
--best \
--tryhard \
--solexa1.3-quals \
--chunkmbs 128 \
hg19 \
-1 dodgy_input_1 \
-2 dodgy_input_2 \
--un dodgy_pair_pe_unmatched.bowtie \
--max dodgy_pair_pe_ambiguous.bowtie \
dodgy_pair_pe_matched.bowtie \
&> dodgy_pair_pe_console.out
Results:
For the independent search, I get 12,637 matches to end #1 and 13,946 matches to end #2.
For the paired search, I get 919 pairs (although I expected 393 since that many pair combinations from the original results can be combined to form pairs that satisfy -I and -X).
Example of result pair that has a mapping for end #2 that did not appear in the independent search:
HWI-EAS283:2:1:810:1386#0/1 + chr11 107533126 GGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCTG >C;AABBBCCCCCAC9A@CBCCBBABCCABBBBBBAABBB 344
HWI-EAS283:2:1:810:1386#0/2 - chr11 107533223 TACTCAGGAGGCTGAGGCAGGAGAATTGGTTGAACCCGGG CBCBCCBBBB@>CCCBCACCBCBCCCCABBCBCBC;@B@B 344 11:C>G,13:C>T
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