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Forum: RNA Sequencing 07-27-2015, 06:52 AM
Replies: 12
Views: 2,125
Posted By arash82
@SNPsaurus: All the libraries are made...

@SNPsaurus: All the libraries are made individually. Then the samples are pooled and sequenced.

@GenoMax: Core facility cannot figure it out either. Very unlikely we would do this from scratch....
Forum: RNA Sequencing 06-26-2015, 06:10 AM
Replies: 12
Views: 2,125
Posted By arash82
Processing all the data, it seems the...

Processing all the data, it seems the contamination only exists among samples that have one of the two barcodes the same.

For instance, sample 1 and 2 both have the same index 2, but different...
Forum: RNA Sequencing 06-26-2015, 05:38 AM
Replies: 12
Views: 2,125
Posted By arash82
I have a total of 17 samples, 12 different index...

I have a total of 17 samples, 12 different index 1 and 8 different index 2. Samples are all mixed and ran in 4 lanes.


The numbers I gave are just line counts. To get a real representation, I...
Forum: RNA Sequencing 06-26-2015, 01:53 AM
Replies: 12
Views: 2,125
Posted By arash82
Obviously, I have more than two samples and I...

Obviously, I have more than two samples and I feel it is going to be a nightmare investigating all the barcodes in all the samples =S

Just comparing the first mate of these two samples and two...
Forum: RNA Sequencing 06-26-2015, 01:36 AM
Replies: 12
Views: 2,125
Posted By arash82
Thanks for the reply. I havenít done the wet...

Thanks for the reply.

I havenít done the wet part, but I am a bit doubtful regarding chimeric molecules. When the tubes are attached the molecules are in different tubes so I donít see how index 1...
Forum: RNA Sequencing 06-25-2015, 07:20 AM
Replies: 12
Views: 2,125
Posted By arash82
Adapters and multiplexing

I am trying to trim adapaters and there is a thing that doesn't quite make sense to me. I've done some simplifications in the description here to focus on the issue. Thanks in advance for any help on...
Forum: Bioinformatics 06-11-2015, 04:42 AM
Replies: 4
Views: 1,614
Posted By arash82
Well, it is all handled by the core facility, so...

Well, it is all handled by the core facility, so I am rather handicapped here and still learning. I gave them purified transcripted mRNA. Checking my notes it actually says they made the library with...
Forum: Bioinformatics 06-11-2015, 04:34 AM
Replies: 4
Views: 1,614
Posted By arash82
Thanks Brian. It is a good point. Just...

Thanks Brian. It is a good point.

Just doing a adapter seque line count in mate 1 I get the following results:
Forward: 12 204
Reverse: 4 600

Obviously much less reverese, but still doesn't...
Forum: Bioinformatics 06-05-2015, 02:28 AM
Replies: 4
Views: 1,614
Posted By arash82
Reverese complement adapter in mate 1

Hi,

I am still quite a noob at this, so bear with me.

I have some RNA Seq PE-50 data and I am trying to do some adapter trimming. Library was made with a Smarter Race Kit. I was thinking to...
Forum: Bioinformatics 02-13-2015, 07:26 AM
Replies: 20
Views: 7,845
Posted By arash82
Dear Brian, Thanks for the extensive...

Dear Brian,

Thanks for the extensive response and clarification on how the program works. Very much appreceated.

I kind of forgot to mention that I am using it on RNA-seq data from a HiSeq...
Forum: Bioinformatics 02-11-2015, 08:36 PM
Replies: 20
Views: 7,845
Posted By arash82
First, thanks Brian for this tool... I am trying...

First, thanks Brian for this tool... I am trying to use it on pilot data to determine how to multiplex my samples.

To my question, I am not entire sure I understand how to interpret the results.
...
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