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Old 03-05-2010, 12:05 AM   #1
dina
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Location: israel

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Hi,
I have a strange problem: some of the contigs receive exact match in blast but when usin blat there is a big gap which might be interesting for me ( a mutation? a big part of the gene is missing). So..? How can I know whether this gap exists or no? why in blast the whole contig is mapped to a reference while in blat there is a gap in the middle?
Thank you!
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Old 03-06-2010, 01:28 PM   #2
jmartin127
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Did you check to make sure that BLAST is aligning the full length of the contig?
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