Forum: Bioinformatics
09-15-2014, 03:33 AM
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Replies: 3
Views: 2,039
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Forum: Bioinformatics
09-15-2014, 02:48 AM
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Replies: 3
Views: 2,039
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...
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Forum: Bioinformatics
10-19-2011, 06:41 AM
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Replies: 36
Views: 20,203
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...
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Forum: RNA Sequencing
02-21-2011, 12:11 AM
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Replies: 7
Views: 3,258
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...
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Forum: RNA Sequencing
02-18-2011, 04:59 AM
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Replies: 7
Views: 3,258
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Forum: RNA Sequencing
02-11-2011, 05:34 AM
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Replies: 15
Views: 6,867
@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...
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Forum: RNA Sequencing
02-11-2011, 04:59 AM
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Replies: 7
Views: 3,258
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...
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Forum: Core Facilities
11-29-2010, 12:26 AM
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Replies: 12
Views: 7,063
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Forum: Bioinformatics
10-14-2010, 07:29 AM
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Replies: 0
Views: 1,328
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...
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Forum: Illumina/Solexa
08-03-2010, 12:30 AM
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Replies: 4
Views: 3,756
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...
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Forum: RNA Sequencing
07-30-2010, 07:35 AM
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Replies: 3
Views: 3,846
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Forum: Illumina/Solexa
07-30-2010, 07:20 AM
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Replies: 4
Views: 3,756
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...
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Forum: Core Facilities
07-30-2010, 06:31 AM
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Replies: 12
Views: 7,063
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...
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Forum: Sample Prep / Library Generation
07-30-2010, 03:34 AM
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Replies: 2
Views: 3,808
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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