Forum: Bioinformatics
04-05-2012, 11:44 AM
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Replies: 1
Views: 2,029
Maq error after using cutadapt
I have some small RNA data, generated with a GAIIx, and I need to trim the adapter sequence off the 3' end. I used cutadapt, which seemed easy enough, but now I can't get the trimmed sequences to...
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Forum: Illumina/Solexa
08-02-2011, 04:17 PM
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Replies: 0
Views: 2,409
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Forum: Core Facilities
03-15-2011, 03:24 PM
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Replies: 5
Views: 3,487
how MUCH data do you give back?
Hi all!
We're a relatively new core running Illumina's GAIIx and I'm trying to deal with the issue of data. Typically once the customers run finishes and if they want me to do the alignment I run...
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Forum: Illumina/Solexa
01-19-2011, 01:24 PM
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Replies: 32
Views: 24,165
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Forum: Sample Prep / Library Generation
12-10-2010, 09:18 AM
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Replies: 3
Views: 2,845
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Forum: Sample Prep / Library Generation
12-10-2010, 08:23 AM
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Replies: 3
Views: 2,845
ChIPseq: Strange Peaks after Gel Extraction
x-posted from general: i didn't realize i posted in the wrong forum until today.
Hi,
I've been doing ChIP library preps for a good while now and never before have I seen anything like this and...
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Forum: Sample Prep / Library Generation
12-09-2010, 02:16 PM
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Replies: 9
Views: 5,037
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Forum: General
12-09-2010, 02:04 PM
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Replies: 1
Views: 2,190
ChIPseq: Strange Peaks after Gel Extraction
Hi,
I've been doing ChIP library preps for a good while now and never before have I seen anything like this and was hoping someone maybe has?
I am seeing two peaks in my samples. One at around...
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Forum: Illumina/Solexa
12-01-2010, 09:02 AM
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Replies: 28
Views: 13,109
Thanks for this info. Super helpful. How are...
Thanks for this info. Super helpful. How are you using the Ambion frag buffer then? Are you starting with 50 - 100ng of mRNA? Are you following Ambions protocol for 70C x 15 minutes? And in what...
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Forum: Illumina/Solexa
09-08-2010, 09:29 AM
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Replies: 28
Views: 13,109
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Forum: Illumina/Solexa
09-07-2010, 08:48 PM
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Replies: 28
Views: 13,109
Hi all,
I am looking at the directional...
Hi all,
I am looking at the directional protocol now and see that it requires the v1.5 sRNA 3' Adaptor. Which adaptor is this? I'm assuming it is NOT the Small RNA 3' adaptor.
Thanks!
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Forum: Illumina/Solexa
08-12-2010, 10:48 AM
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Replies: 17
Views: 9,917
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Forum: Illumina/Solexa
08-12-2010, 09:33 AM
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Replies: 17
Views: 9,917
We ended up spiking with 30% PhiX (at 7.5pM)...
We ended up spiking with 30% PhiX (at 7.5pM) because we realized spiking in such a low % of PhiX wouldn't help. Doesn't look like the 30% helped much either since Pipeline is having a hard time with...
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Forum: Illumina/Solexa
07-21-2010, 11:01 AM
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Replies: 17
Views: 9,917
When do you add your PhiX to the sample? I'm...
When do you add your PhiX to the sample? I'm assuming if it's already at a pM concentration then it's after denaturation and you're adding PhiX diluted in HT1 to your samples that are denatured and...
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Forum: Sample Prep / Library Generation
03-24-2010, 08:55 AM
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Replies: 3
Views: 4,410
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