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Search: Posts Made By: NeleZ
Forum: Bioinformatics 01-05-2015, 01:18 AM
Replies: 3
Views: 2,345
Posted By NeleZ
in case you haven't solved it yet: you have to...

in case you haven't solved it yet:
you have to re-run cuff<-readCufflinks() to initialize the database
only if no cuffData.db database is present the command builds it from scratch, otherwise it...
Forum: Bioinformatics 10-16-2014, 01:35 AM
Replies: 3
Views: 2,345
Posted By NeleZ
cummerbund error: expired SQLiteConnection

Hi,

I'm using cummeRbund and it's working fine, only that after reloading the R workspace I cannot access the database anymore but I get an error saying:
Error in sqliteExecStatement(con,...
Forum: RNA Sequencing 10-16-2014, 01:07 AM
Replies: 7
Views: 2,524
Posted By NeleZ
hi blancha, you say I don't have to rebuild the...

hi blancha,
you say I don't have to rebuild the database. However I get an error message when trying to access the database (via the pointer object "cuff") after reloading it:
"Error in...
Forum: Vendor Forum 07-23-2014, 01:25 AM
Replies: 40
Views: 17,293
Posted By NeleZ
I do the size selection after the amplification...

I do the size selection after the amplification and I use polyA selection
Forum: Vendor Forum 07-22-2014, 07:54 AM
Replies: 40
Views: 17,293
Posted By NeleZ
I also get very low yields for my library after...

I also get very low yields for my library after 15 cycles of PCR (~5-15ng/ul) although I start with ~4ug total RNA i.e. ~100ng polyA. Same for others in our lab.
This seems really low to what other...
Forum: RNA Sequencing 02-13-2014, 02:47 AM
Replies: 23
Views: 18,583
Posted By NeleZ
@simonandrews hi, has this option been added...

@simonandrews
hi, has this option been added yet? I'd also be interested in using it... or would it be possible to have the transcriptome instead of the genome as a reference to remove the up and...
Forum: Sample Prep / Library Generation 12-09-2013, 07:48 AM
Replies: 0
Views: 1,358
Posted By NeleZ
Narrow vs broad size selection

Hello,

I have a question regarding the purpose of the size selection.
Apart from the more obvious reason to exclude adapter/primer dimers, the mapping of paired-end data requires a defined insert...
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