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Search: Posts Made By: windhorse8
Forum: Bioinformatics 03-27-2015, 07:56 AM
Replies: 11
Views: 4,912
Posted By windhorse8
Hi Dariober, The fastQ file was sent by our...

Hi Dariober,
The fastQ file was sent by our collaborator who did the sequencing. I don't know if they went through Miseq pipeline. However, based on what you are saying and info provided in the link...
Forum: Bioinformatics 03-26-2015, 02:34 PM
Replies: 11
Views: 4,912
Posted By windhorse8
Hi Brian, Please find the dropbox link for...

Hi Brian,
Please find the dropbox link for FastQC report for my data.
https://www.dropbox.com/s/4i9642io1gk7ru0/KR3_S1_L001_R1_001.fastq%20FastQC%20Report.pdf?dl=0
The 3' adapter ligated sRNA...
Forum: Bioinformatics 03-26-2015, 12:34 PM
Replies: 11
Views: 4,912
Posted By windhorse8
Too many reads containing all N's in Miseq read

Dear All,
I recently used Miseq for small RNA library sequencing (single end, 35 cycle). The library was prepared using size selected (19-24 nt) small RNA sequences. When I analyzed the result...
Forum: Illumina/Solexa 09-15-2014, 06:16 AM
Replies: 43
Views: 28,548
Posted By windhorse8
Hi ZAAB, Are there any other unique...

Hi ZAAB,
Are there any other unique specifications to be followed for the synthesis of custom primers beside Tm such as requirements for HPLC/PAGE purifications or inclusion of phosphorothioate...
Forum: Illumina/Solexa 09-15-2014, 06:13 AM
Replies: 4
Views: 3,265
Posted By windhorse8
Hi kwaraska, Are there any unique...

Hi kwaraska,
Are there any unique specifications for the synthesis of custom primers such as the requirement of HPLC/PAGE purification, or inclusion of phosphorothioate bonds in the primers ? My...
Forum: Sample Prep / Library Generation 08-12-2014, 09:55 AM
Replies: 5
Views: 4,229
Posted By windhorse8
How about NEBnext multiplex small RNA library...

How about NEBnext multiplex small RNA library prep set (cat. no. E7330S) ? Is library prepared using this kit also compatible with Miseq ? Do I have to send separate custom primer since custom primer...
Forum: Illumina/Solexa 08-11-2014, 07:18 AM
Replies: 55
Views: 32,054
Posted By windhorse8
What's the full reference details for Caporaso...

What's the full reference details for Caporaso PNAS paper?
Is Caporaso's P5 and P7 sequences compatible on Miseq flowcell too?
Forum: Illumina/Solexa 08-08-2014, 08:01 AM
Replies: 7
Views: 4,153
Posted By windhorse8
Hi Scott, Thanks for your reply. I am...

Hi Scott,
Thanks for your reply.
I am wondering if you published your work ? I have been looking for publications ( preferably methods paper) that have used custom primers and adapters to prepare...
Forum: Illumina/Solexa 08-07-2014, 10:56 AM
Replies: 43
Views: 28,548
Posted By windhorse8
But what about P5 and P7 sequence for Miseq. If I...

But what about P5 and P7 sequence for Miseq. If I understand correctly, the actual P5 and P7 sequences attached on flow cells are different between Hiseq and Miseq. I also need to make library using...
Forum: Illumina/Solexa 08-07-2014, 10:47 AM
Replies: 7
Views: 4,153
Posted By windhorse8
Hi, I am wondering if you were able to...

Hi,
I am wondering if you were able to successfully design custom primers for Miseq. I am also planning to do similar thing. Wondering how did your go or if you can shed some knowledge about it ?
Forum: Illumina/Solexa 08-07-2014, 10:37 AM
Replies: 22
Views: 11,197
Posted By windhorse8
Do you construct the library (3' adapter ligation...

Do you construct the library (3' adapter ligation and so forth) using small RNA sample prep kit or using your own adapters, primers, and other reagents. I am also making libraries but I have to use...
Forum: Illumina/Solexa 08-07-2014, 09:18 AM
Replies: 37
Views: 42,048
Posted By windhorse8
I looked at the sequences for pair-end in the...

I looked at the sequences for pair-end in the nature paper you referred to. The sequences are different from what we had designed. However, these sequences from the paper are also different from what...
Forum: Illumina/Solexa 08-07-2014, 07:45 AM
Replies: 37
Views: 42,048
Posted By windhorse8
I think I also have similar problem. Can anyone...

I think I also have similar problem. Can anyone help ?
We recently sent small RNA library prepared using adapters, and primers bought from IDT ( not Illumina kit) for high throughtput sequencing...
Forum: Illumina/Solexa 09-12-2013, 11:00 AM
Replies: 3
Views: 4,510
Posted By windhorse8
low complexity PCR amplicon sequencing using Miseq

Hi All,
I need to use Miseq for sequencing a pool of multiplexed PCR amplicons through in-house PCR amplicon preparation procedure (for various reasons) using custom-ordered adapters and primers....
Forum: Illumina/Solexa 08-08-2013, 11:03 AM
Replies: 3
Views: 3,517
Posted By windhorse8
Primer and adapter design for small RNA sequencing in HiSeq2000 and MiSeq

Hi,
I need to sequence pools of small RNA (each pool with varying size ranging from 20-100 bases, so planning to use barcode for each pool) using Hiseq2000 or MiSeq. I don't have in-house access for...
Forum: Service Providers 07-18-2011, 10:20 AM
Replies: 20
Views: 24,112
Posted By windhorse8
Car pools provider

Hello,
Would you be able to remember who does this "Car pool". We want to do sequencing but cost is one of the limiting factors currently. Therefore, we are looking for car pools and also any...
Forum: 454 Pyrosequencing 07-18-2011, 09:04 AM
Replies: 1
Views: 1,568
Posted By windhorse8
454 sequencing institutions/companies

Hi,
We are looking for institutions or companies willing to sequence our PCR product. We request any institutions or companies who have free slots for sequencing our PCR products using 454 platform...
Forum: Introductions 05-27-2011, 11:27 AM
Replies: 0
Views: 1,401
Posted By windhorse8
Sequencing PCR products

Hello to all,

I am trying to find information about sequencing pcr products that I made from my RNA transcript. I am wondering if I could use it directly for sequencing using Illumina or other...
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