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Old 02-23-2009, 08:18 PM   #1
baohua100
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Default maq pair end alignment error

maq pair end alignment error

maq map out.map re.bfa pair1.bfq pair2.bfq

-- maq-0.6.3
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 41.
[ma_load_reads] set length of the second read as 41.
maq: read.cc:59: longreads_t* ma_load_reads(void*, int, void*, int): Assertion `strcmp(name, lr->name[j]) == 0' failed.
Aborted


what's the problem?
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Old 02-24-2009, 08:40 AM   #2
bioinfosm
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Any specific reason for using the much older 0.6.3? Sorry not sure of why the error though..
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Old 02-24-2009, 06:14 PM   #3
baohua100
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pair1.fq:
@seq1_1
CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTT
+seq1_1
hhYhhRhhhhhhhhfhh`ThhdhXTaVNWJLKGgcKGgcKG
@seq2_1
TAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAA
+seq2_1
hhchh[h]hhhhhVhhhhLhdhhgPPhhUSYOOPQYOOPQQ
@seq3_1
AATCCTACATCCATGAATCCCTAAATACCTAATTCCCTAAA
+seq3_1
hhhhhhhhhhhhYPhhhhhKhhhTacNhhOF]IIDOF]IID

pair2.fq:
@seq1_2
ACAAATCCTATTTCTTGTGGTTTTCTTTCCTTCACTTAGCT
+seq1_2
hhYhhRhhhhhhhhfhh`ThhdhXTaVNWJLKGgcKGgcKG
@seq2_2
GTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCAT
+seq2_2
hhchh[h]hhhhhVhhhhLhdhhgPPhhUSYOOPQYOOPQQ
@seq3_2
CGAGCACACACACACGGTGGCTATCATCGATCGATCGATGC
+seq3_2
hhhhhhhhhhhhYPhhhhhKhhhTacNhhOF]IIDOF]IID

maq-0.7.1/maq map out.map re.bfa pair1.bfq pair2.bfq

results:
seq1_1 ref 1 + 223 1 61 61 61 0 0 1 0
41 CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTT ``Y``R````````````T````XT`VNWJLKG``KG``KG
seq2_1 ref 18 + 225 1 61 61 61 0 0 1 0
41 TAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAA `````[`]`````V````L`````PP``USYOOPQYOOPQQ
seq3_1 ref 66 + 0 64 61 61 0 0 0 1 0
41 AATCCTACATCCATGAATCCCTAAATACCTAATTCCCTAAA ````````````YP`````K```T``N``OF]IIDOF]IID
seq3_1 ref 66 + 0 192 0 0 0 0 0 0 0
41 CGAGCACACACACACGGTGGCTATCATCGATCGATCGATGC ````````````YP`````K```T``N``OF]IIDOF]IID
seq1_1 ref 223 + -223 1 61 61 61 0 0 1 0
41 ACAAATCCTATTTCTTGTGGTTTTCTTTCCTTCACTTAGCT ``Y``R````````````T````XT`VNWJLKG``KG``KG
seq2_1 ref 242 + -225 1 61 61 61 0 0 1 0
41 GTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCAT `````[`]`````V````L`````PP``USYOOPQYOOPQQ

it's strange! the read id , the mapping position 66
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Old 02-25-2009, 01:14 AM   #4
lh3
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You should change your read name to:

seq1/1, seq1/2
seq2/1, seq2/2

MAQ needs to parse the read names to get pairing. Sorry for the inconvenience.
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Old 02-25-2009, 07:56 PM   #5
baohua100
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Thanks for your reply! Now I get new result:

seq1/1 ref 1 + 164 1 61 61 61 0 0 1 0 35 C
CCTAAACCCTAAACCCTAAACCCTAAACCTCTGA ``Y``R````````````T````XT`VNWJLKG``
seq2/1 ref 40 + 208 1 61 61 61 0 0 1 0 35 T
TAATCCCTAAATCCCTAAATCTTTAAATCCTACA `````[`]`````V````L`````PP``USYOOPQ
seq3/1 ref 79 + 0 192 0 0 0 0 0 0 0 35 G
GGGGGGGGGGGGGCCCCCCCCCCCCCCCCCCCCC ````````````YP`````K```T``N``OF]IID
seq3/2 ref 79 + 0 64 61 61 0 0 0 1 0 35 T
GAATCCCTAAATACCTAATTCCCTAAACCCGAAA `]`````V````L`````PP``USYOOPQYOOPQQ
seq1/2 ref 164 + -164 1 61 61 61 0 0 1 0 35 T
TTTATGTAATTGCTTATTGTTGTGTGTAGATTTT ````````````T````XT`VNWJLKG``KG``KG
seq2/2 ref 247 + -208 1 61 61 61 0 0 1 0 35 C
TTTCCTTCACTTAGCTATGGATGGTTTATCTTCA ````````````YP`````K```T``N``OF]IID

seq3/2 align on postion 79 , seq3/1 could not aligned but Maq also display it.
How Maq output pair read alignment?
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