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Forum: Bioinformatics 01-26-2011, 02:59 AM
Replies: 7
Views: 5,641
Posted By michy
Hello fkrueger, I've never tried this software...

Hello fkrueger,
I've never tried this software but I will now, it looks very useful.

Thank you,
Michy
Forum: Bioinformatics 01-26-2011, 02:12 AM
Replies: 7
Views: 5,641
Posted By michy
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...
Forum: Bioinformatics 01-26-2011, 01:09 AM
Replies: 7
Views: 5,641
Posted By michy
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...
Forum: Bioinformatics 09-02-2010, 06:07 AM
Replies: 1
Views: 1,999
Posted By michy
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...
Forum: Bioinformatics 12-09-2009, 08:41 AM
Replies: 3
Views: 2,058
Posted By michy
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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