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Forum: Ion Torrent 06-13-2019, 05:35 AM
Replies: 2
Views: 807
Posted By scubachris
Ion Torrent Proton PII-PIII Chips?

Hello,

apologies about the simplicity of the question but I'm a bit out of the loop and I couldn't find any relevant info online. Back in 2013 I used to work at a lab that had an Ion Torrent...
Forum: RNA Sequencing 05-08-2019, 03:25 AM
Replies: 2
Views: 796
Posted By scubachris
For example to see if housekeeping genes with...

For example to see if housekeeping genes with high expected expressions are indeed so across all samples.
Thank you, I will have a look at this program.
Forum: RNA Sequencing 05-07-2019, 10:39 PM
Replies: 2
Views: 796
Posted By scubachris
Quick way to QC processed RNA-Seq data

Greetings,

Is there some software/library that will automatically perform a data consistency check and possibly heatmaps on processed RNA-Seq datasets from GEO?
(for example...
Forum: De novo discovery 02-23-2011, 05:53 AM
Replies: 6
Views: 3,654
Posted By scubachris
Hi, thanks a lot for the reply! I'm afraid the...

Hi, thanks a lot for the reply! I'm afraid the problem is with the coverage, hopefully we'll be doing some more sequencing soon! I didn't see much difference in the results of Velvet, ABySS, or CLC,...
Forum: De novo discovery 02-17-2011, 04:51 AM
Replies: 6
Views: 3,654
Posted By scubachris
Hello again, I managed to do a decent filtering...

Hello again,
I managed to do a decent filtering by trimming trailing 'B's and excluding reads with Phred < 20.
After running a De novo assembly with CLC Genomics Workbench, I got some contigs with...
Forum: De novo discovery 02-04-2011, 07:28 AM
Replies: 6
Views: 3,654
Posted By scubachris
Hello, thanks a lot for the reply! I'll have a...

Hello, thanks a lot for the reply! I'll have a look at both programs!
As for the low quality reads, since my coverage wasn't much (around 15), I was trying to be somewhat parsimonious, so I did...
Forum: De novo discovery 01-23-2011, 02:45 AM
Replies: 6
Views: 3,654
Posted By scubachris
OK, so far I am replacing all low quality bases...

OK, so far I am replacing all low quality bases with "N", so I don't have to trim anything. Still, any other ideas are welcome....
Forum: De novo discovery 01-22-2011, 06:43 AM
Replies: 6
Views: 3,654
Posted By scubachris
Paired-end questions

Greetings to all!
I was recently given some sequencing data for a not yet sequenced organism, so I am trying a de-novo assembly with Velvet. This is the first time I've been working with sequencing...
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