Forum: Bioinformatics
01-26-2011, 02:59 AM
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Replies: 7
Views: 5,635
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Forum: Bioinformatics
01-26-2011, 02:12 AM
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Replies: 7
Views: 5,635
Hello fkrueger,
thank you for your reply. Your...
Hello fkrueger,
thank you for your reply. Your suggestions esp. a) and c) they did improve the alignment by 15% which means 85% still failed to align. However, I was testing the command on a small...
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Forum: Bioinformatics
01-26-2011, 01:09 AM
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Replies: 7
Views: 5,635
Bowtie and reads that failed to align: (100.00%)
Hello,
Can someone help me please. I have some new paired-end sequence from illumina and the reads are not aligning. What am I doing wrong? An example of the reads are below with the commandline...
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Forum: Bioinformatics
09-02-2010, 06:07 AM
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Replies: 1
Views: 1,999
bowtie and solexa paired ends wont align
Hello,
I am trying to align paired end reads from Solexa using Bowtie, the command is below. But, this does not work and we get 4% reads aligned. If we use the sequences/reads not paired we get...
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Forum: Bioinformatics
12-09-2009, 08:41 AM
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Replies: 3
Views: 2,054
MAQ and SNP calling
Hello,
I've used MAQ to call SNPs in Illumina data, it worked fine apart from the read depth. When I looked at the alignment using IGV the read depth is often alot more. Im sure theres a reason,...
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