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Search: Posts Made By: CindyF
Forum: General 11-10-2014, 07:30 AM
Replies: 0
Views: 1,197
Posted By CindyF
Creating a customized reference genome for genome analysis?

Hi everyone,

I was just wondering something that I would like to discuss with experts - or at least those that are more expert in that area than myself as a newbie. ;) I was not quite sure into...
Forum: Bioinformatics 01-16-2014, 08:44 AM
Replies: 9
Views: 7,184
Posted By CindyF
Hi everyone, so finally I got in contact...

Hi everyone,

so finally I got in contact with someone from illumina to get some more information about their Amplicon Analysis Workflow. Only to find out that alignment and variant calling is...
Forum: Bioinformatics 01-06-2014, 03:48 AM
Replies: 9
Views: 7,184
Posted By CindyF
Hi everyone, @dnusol: Unfortunately I cannot...

Hi everyone,

@dnusol: Unfortunately I cannot help you with your issue because I am not yet familiar with amplicon analysis. :/

@all: I finally found out that a somatic variant caller is used in...
Forum: Bioinformatics 12-02-2013, 11:14 PM
Replies: 9
Views: 7,184
Posted By CindyF
Thanks lebechec and GenoMax for the information....

Thanks lebechec and GenoMax for the information. I'll dive deeper into the topic and see how well I can actually apply the algorithms used by MiSeq.

Best,

CindyF
Forum: Bioinformatics 12-02-2013, 05:07 AM
Replies: 9
Views: 7,184
Posted By CindyF
Hi lebechec, have you received more...

Hi lebechec,

have you received more information from Illumina regarding the internal analysis pipeline that is used in MiSeq? I would also like to be able to reproduce the results coming from...
Forum: Bioinformatics 09-12-2013, 11:21 PM
Replies: 3
Views: 4,162
Posted By CindyF
Hi lh3, thanks for the link, I have not come...

Hi lh3,

thanks for the link, I have not come across it yet. It is quite interesting to see that run time performance indeed seems to be a challenge for variant calling.

Regarding your overnight...
Forum: Bioinformatics 09-12-2013, 08:56 AM
Replies: 3
Views: 4,162
Posted By CindyF
Question Run Time Performance of Variant (SNP) Calling Tools?

Hi all,

I read lots of papers about SNP calling and the different implementations (GATK, SAMtools, SOAPsnp, etc) in the last time. Something I noticed was that in no paper run time performances...
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