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Forum: Pacific Biosciences 02-14-2014, 05:58 AM
Replies: 4
Views: 5,634
Posted By curious.genome
Do we have any updates on this ? Has the OP...

Do we have any updates on this ? Has the OP figured out how to get FALCON working ?
Forum: Pacific Biosciences 11-13-2013, 09:29 AM
Replies: 1
Views: 1,732
Posted By curious.genome
So I'm going to try to answer my own question. I...

So I'm going to try to answer my own question. I spoke to a PacBio rep yesterday, and from what I gather, it seems like they have an HMM that models the quality of each position in the CCS based on...
Forum: Pacific Biosciences 11-11-2013, 08:12 AM
Replies: 1
Views: 1,732
Posted By curious.genome
Read quality calculation for a base in CCS

Hi guys,

I was wondering if anyone could tell me how PacBio calculates the quality scores while generating CCS sequences.

For example, suppose a particular base has 3 passes, and so we get 3...
Forum: Illumina/Solexa 10-24-2013, 10:41 PM
Replies: 8
Views: 2,611
Posted By curious.genome
Thanks for the sound advice, mcnelson. I'll go...

Thanks for the sound advice, mcnelson. I'll go ahead with the assembly for now
Forum: Pacific Biosciences 10-24-2013, 10:39 PM
Replies: 3
Views: 14,122
Posted By curious.genome
Thanks for taking the time to explain that,...

Thanks for taking the time to explain that, mcnelson, it definitely helps ! I can now proceed to my next step - investigating how to work with the HGAP assembler.

GenoMax thanks for the links to...
Forum: Illumina/Solexa 10-24-2013, 11:13 AM
Replies: 8
Views: 2,611
Posted By curious.genome
Thanks mcnelson ! For now, all I plan to do with...

Thanks mcnelson ! For now, all I plan to do with the reads is to perform assembly. I am not interested in variants/etc. I planned on removing the duplicates to aid the assembler. Is this a bad idea ?
Forum: Pacific Biosciences 10-24-2013, 09:41 AM
Replies: 3
Views: 14,122
Posted By curious.genome
PacBio CCS vs subreads explained ?

Hi guys,

I've been trying to understand PacBio data for a while now, I think that it's the way forward for our lab. I'm still having trouble understanding CCS though - my biology is quite shaky. ...
Forum: Illumina/Solexa 10-24-2013, 09:26 AM
Replies: 8
Views: 2,611
Posted By curious.genome
Thanks mcnelson, I missed your reply. I'l have a...

Thanks mcnelson, I missed your reply. I'l have a go at mothur too, but like you said, I need a fix for the sub 100% match as well.
Forum: Illumina/Solexa 10-24-2013, 09:24 AM
Replies: 8
Views: 2,611
Posted By curious.genome
That was quick! Thanks Vivek, I'll try fastx...

That was quick! Thanks Vivek, I'll try fastx collapser.

From a quick google search, it looks like this tool can only collapse completely identical reads. I might still want to figure out how to...
Forum: Illumina/Solexa 10-24-2013, 09:11 AM
Replies: 8
Views: 2,611
Posted By curious.genome
Duplicate removal without alignment to reference genome

Hi guys,

So our HiSeq data is showing a large number of duplicate sequences. I've come across tools like Picard MarkDups or samtools rmdup which remove duplicates - however they seem to require...
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