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We would like to ask whether anyone else has seen the same problems when using 454's gsMapper with a set of reads and a reference sequence. How can one reduce the number of gaps that were introduced by the mapping alogrithm?
Problem 1:
In the ace file, one often sees gaps introduced by gsMapper at the begin of a read that could be perfectly aligend to the reference sequence. We think that this gap is a bug in the algorithm and should be avoided. Is there a gsMapper parameter that can be modified in order to prevent such gaps? Gaps are introduced only at the begin of a read, not at the end.
Problem 2:
At another position in the ace file, gsMapper inserts gaps to avoid a mismatch. We want that the alignment has higher priority than inserting gaps. Is there a parameter in gsMapper that prevents such gaps? In the cases shown below, we prefer a mismatch than a gap.
Many thanks for help!
Problem 1:
In the ace file, one often sees gaps introduced by gsMapper at the begin of a read that could be perfectly aligend to the reference sequence. We think that this gap is a bug in the algorithm and should be avoided. Is there a gsMapper parameter that can be modified in order to prevent such gaps? Gaps are introduced only at the begin of a read, not at the end.
HTML Code:
read_1 GTCCGTTGCTTTAAGTGCTTGTTTATTCAT read_2 GTCCGTTGCTTTAAGTGCTTGTTTATTCAT read_3 GTCCGTTGCTTTAAGTGCTTGTTTATTCAT read_4 GTCCGTTGCTTTAAGTGCTTGTTTATTCAT read_5 GTCCGTTGCTTTAAGTGCTTGTTTATTCAT read_6 GTCCGTTGCTTTAAGTGCTTGTTTATTCAT read_7 TTGCTTTAAGTGCTTGTTTATTCAT read_8 TTGCTTTAAGTGCTTGTTTATTCAT read_9 GTCCGTTGCTTTAAGTGCTTGTTTATTCAT read_10 C.GTTGCTTTAAGTGCTTGTTTATTCAT read_11 TT.ATTCAT read_12 T.CAT contig GTCCGTTGCTTTAAGTGCTTGTTTATTCAT ref GTCcGTTGCTTTAAGTGCTTGTTtATtCAT
Problem 2:
At another position in the ace file, gsMapper inserts gaps to avoid a mismatch. We want that the alignment has higher priority than inserting gaps. Is there a parameter in gsMapper that prevents such gaps? In the cases shown below, we prefer a mismatch than a gap.
HTML Code:
read_1 CC.AGAAACG.AGGAGACTCTTGGGA.TAGCGCCAAG.TCA read_2 CC.AGAAACG.AGGAGACTCTTGGGA.TAGCGCCAAG.TCA read_3 CC.AGAAACG.AGGAGACTCTTGGGA.TAGCGCCAAG.TCA read_4 CCN.GAAACGN.GGAGACTCTTGGGA.TAGCG read_5 CC.AGAAACGN.GGAGACTCTTGGGA.TAGCGCCAAG.TCA read_6 CC.AGAA.CG.AGGAGACTCTTGGGA.TAGCGCCAAG.TCA read_7 CC.AGAAACG.AGGAGACTCTTGGGA.TAGCGCCAAG.TCA read_8 CC.AGAAACG.AGGAGA read_9 CC.AGAAACG.AGGAGAC read_10 CC.AGAAACG.AGGAGACTC read_11 CC.AGAAACG.AGGAGACTCTTGGGA.TAGCGCCAAG.TCA read_12 CC.AGAAACG.AGGAGACTCTTGGGA.TAGCGCCAAG.TCA read_13 CC.AGAAACG.AGGAGACTCTTGGGA.TAGCGCCAAG.TCA read_14 G.AGGAGACTCTTGGGA.TAGCGCCAAG.TCA read_15 AGGAGACTCTTGGGA.TAGCGCCAAG.TCA read_16 G.AGACTCTTGGGA.TAGCGCCAAGC.CA read_17 CTCTTGG.AATAGCGCCAAG.TCA read_18 TAGCGCCAAG.TCA read_19 A.G.TCA contig CC.AGAAACG.AGGAGACTCTTGGGA.TAGCGCCAAG.TCA ref CC-aGAAaCG-aGgAGACTCTTGGgA-TAGCGCCAaG-tCA
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