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Forum: Bioinformatics 09-15-2014, 03:33 AM
Replies: 3
Views: 2,070
Posted By nasobema
OK, sure. But then, there wouldn't be the option...

OK, sure. But then, there wouldn't be the option to separate the feature types any more. Unless I maintain multiple annotation files, of course.

Seems like I have to stick to workarounds.
Forum: Bioinformatics 09-15-2014, 02:48 AM
Replies: 3
Views: 2,070
Posted By nasobema
htseq-count: how to use multiple features?

From the documentation I can only find how to select a certain type of feature for counting, like "exon" (default) or "ncRNA".

Is there also a way to select multiple features?
I'm using it...
Forum: Bioinformatics 10-19-2011, 06:41 AM
Replies: 36
Views: 20,282
Posted By nasobema
Hi earonesty! Thanks a lot for this great...

Hi earonesty!

Thanks a lot for this great tool. I found it just today and the first test with fastq-mcf already left the impression that it is both fast and includes a lot of utilities for...
Forum: RNA Sequencing 02-21-2011, 12:11 AM
Replies: 7
Views: 3,279
Posted By nasobema
Yes, the enzyme works fine on control dsDNA. ...

Yes, the enzyme works fine on control dsDNA.

Incubation temperature was 68 according to the Illumina protocol.
So, could it help to reduce Temperature by a few degrees?
We have currently no...
Forum: RNA Sequencing 02-18-2011, 04:59 AM
Replies: 7
Views: 3,279
Posted By nasobema
Yes, DNA concentration was measured with Qubit,...

Yes, DNA concentration was measured with Qubit, which should be reliable.

Any more ideas?

We have been tightly following the Illumina protocol for DSN. Losing a constant temperate may always be...
Forum: RNA Sequencing 02-11-2011, 05:34 AM
Replies: 15
Views: 6,968
Posted By nasobema
@case 1: I believe it might be because of...

@case 1:
I believe it might be because of methodological bias. Some methods preferentially enrich 5'-ends of mRNAs while others do so for 3'-ends.

Your method is not strand-specific, so you...
Forum: RNA Sequencing 02-11-2011, 04:59 AM
Replies: 7
Views: 3,279
Posted By nasobema
low efficiency of DSN normalization

We have set up a protocol for RNA-seq based on adapter-ligation to RNA-fragments. For ribosome removal, I would like to use the DSN normalization method, which is said to work better than bead-based...
Forum: Core Facilities 11-29-2010, 12:26 AM
Replies: 12
Views: 7,112
Posted By nasobema
No, you have to generate one library per sample,...

No, you have to generate one library per sample, so with your prices, it will sum up to:
12 * ($600 + $50) + $2000 = $7800
Forum: Bioinformatics 10-14-2010, 07:29 AM
Replies: 0
Views: 1,345
Posted By nasobema
Maqview displaying or indexing error

Hi there!

I'm currently using Novoalign to map reads for resequencing and after converting with novo2maq continue with the various Maq tools for SNP and indel discovery.

Sometimes I'm facing a...
Forum: Illumina/Solexa 08-03-2010, 12:30 AM
Replies: 4
Views: 3,780
Posted By nasobema
Expression analysis is indeed one of the...

Expression analysis is indeed one of the applications that we planned.
If the unequal distribution of barcodes is genome wide, I wouldn't expect severe problems because normalization would be...
Forum: RNA Sequencing 07-30-2010, 07:35 AM
Replies: 3
Views: 3,869
Posted By nasobema
What's your recommended RNA fragmentation method?

We already tried
- just heat (95C)
- Mg2+ based buffer with heat
- Zn2+ based buffer with heat

The results were very different with the experiences for Zn2+ (ZnCl2) containing buffer.

Is it...
Forum: Illumina/Solexa 07-30-2010, 07:20 AM
Replies: 4
Views: 3,780
Posted By nasobema
Custom barcoded RNA-seq

Hi,

we are planning on setting up our own custom method for RNA-sequencing with barcodes on an Illimina GAII. I've already found some hints in this forum and elsewhere but still have some...
Forum: Core Facilities 07-30-2010, 06:31 AM
Replies: 12
Views: 7,112
Posted By nasobema
I'm interested in these custom made barcodes. ...

I'm interested in these custom made barcodes.
You would still have to make a full library (including the full cost) for each sample, or wouldn't you?
I'm thinking about a way to use a barcoding...
Forum: Sample Prep / Library Generation 07-30-2010, 03:34 AM
Replies: 2
Views: 3,832
Posted By nasobema
A very interesting study shows some of the...

A very interesting study shows some of the pitfalls of ChIP applications and offers some advances to published protocols.
The paper is dedicated to ChIP on Chip but most of it also applies to...
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