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Forum: Bioinformatics 02-06-2014, 03:06 PM
Replies: 1
Views: 1,237
Posted By chadn737
Bowtie to BWA parameters

I use a pipeline that uses bowtie as the aligner, however, due to genome size, I have had to alter this pipeline to use BWA. I need to run BWA in a way that will give me results equivalent as...
Forum: Bioinformatics 01-31-2014, 10:52 AM
Replies: 11
Views: 7,111
Posted By chadn737
This is for bisulphite-sequencing. The problem...

This is for bisulphite-sequencing. The problem being, that my lab uses a specific pipeline for our analysis, we work closely with the developers. Bowtie is a standard part of that protocol and I have...
Forum: Bioinformatics 01-31-2014, 07:53 AM
Replies: 11
Views: 7,111
Posted By chadn737
An old thread, but I am currently in a similar...

An old thread, but I am currently in a similar situation. I have a polyploid genome of >10 Gbs that I have to work with. Anybody have any recommendations on altering bowtie for this?
...
Forum: Bioinformatics 01-21-2014, 09:03 AM
Replies: 3
Views: 1,637
Posted By chadn737
Did you try emailing the authors about the...

Did you try emailing the authors about the scripts?
Forum: RNA Sequencing 10-21-2013, 07:27 AM
Replies: 6
Views: 1,200
Posted By chadn737
Maybe you mixed up your samples. Do you have...

Maybe you mixed up your samples.

Do you have any evidence, say from independent qPCR or microarrays that would tell you that these genes should be higher expressed. I hate the term "up regulated".
Forum: RNA Sequencing 10-10-2013, 08:44 AM
Replies: 9
Views: 8,624
Posted By chadn737
If you are working on a well sequenced genome and...

If you are working on a well sequenced genome and can map to a reference, then there really is no need to do paired-end if your only goal is differential expression.
Forum: Illumina/Solexa 10-09-2013, 01:25 PM
Replies: 5
Views: 2,040
Posted By chadn737
I would also be interested in knowing how much...

I would also be interested in knowing how much this cost you.
Forum: RNA Sequencing 10-04-2013, 05:37 PM
Replies: 1
Views: 2,322
Posted By chadn737
I have seen similar results. To be honest, I...

I have seen similar results.

To be honest, I trust RNA-seq and microarray results over that of qPCR.
Forum: RNA Sequencing 10-02-2013, 07:09 AM
Replies: 9
Views: 4,655
Posted By chadn737
This isn't a problem. What do you think you are...

This isn't a problem. What do you think you are going to get when you try to do division with zero?
Forum: 454 Pyrosequencing 10-01-2013, 07:10 PM
Replies: 6
Views: 4,019
Posted By chadn737
At 45Mb just sequence the entire genome with...

At 45Mb just sequence the entire genome with Illumina. Depending on the number of samples, you could easily do this at low coverage or even high coverage. 454 is not going to make the bioinformatics...
Forum: RNA Sequencing 09-30-2013, 07:51 PM
Replies: 7
Views: 6,111
Posted By chadn737
If you pool all samples, and split the reads...

If you pool all samples, and split the reads randomly after sequencing then your variation is not due to biological differences, but do to your random sampling. Its going to behave differently.
...
Forum: Bioinformatics 09-24-2013, 03:49 PM
Replies: 26
Views: 13,363
Posted By chadn737
There is a real danger, particularly when you...

There is a real danger, particularly when you combine an attitude of "just give me the end result" and easy to use software, of doing it wrong. A lot of people think that simply because they can do...
Forum: RNA Sequencing 09-23-2013, 02:12 PM
Replies: 2
Views: 1,093
Posted By chadn737
Lots of problems with this design. You loose all...

Lots of problems with this design. You loose all information about biological variation. Don't do it.
Forum: RNA Sequencing 09-22-2013, 01:18 PM
Replies: 2
Views: 1,631
Posted By chadn737
I don't think there are any bam files for these....

I don't think there are any bam files for these. Most of the T-DNA lines early on were mapped using PCR or cloning based methods. Only recently has the Ecker lab started doing sequencing to identify...
Forum: Bioinformatics 09-22-2013, 11:17 AM
Replies: 4
Views: 2,586
Posted By chadn737
If you have access to a server, you might want to...

If you have access to a server, you might want to try it both ways. What organism are you working on? I've messed around with enough polyploid data to know how painful it can be.

The optimal...
Forum: Sample Prep / Library Generation 09-20-2013, 05:54 PM
Replies: 4
Views: 1,901
Posted By chadn737
Essentially this is how some of the libraries...

Essentially this is how some of the libraries were a few years ago...cDNA conversion frist then shearing. It should be noted however, that it was also shown that there is some biases introduced by...
Forum: Bioinformatics 09-11-2013, 08:18 AM
Replies: 2
Views: 2,065
Posted By chadn737
What species are you working in? Methylation is...

What species are you working in? Methylation is very context specific.
Forum: General 09-10-2013, 09:45 AM
Replies: 27
Views: 7,817
Posted By chadn737
That's what I am wondering. I am really trying to...

That's what I am wondering. I am really trying to stop analysis on my laptops anyway, but I still like the flexibility it gives me to be able to do stuff if need too. Although at this point, probably...
Forum: RNA Sequencing 09-10-2013, 09:35 AM
Replies: 4
Views: 1,499
Posted By chadn737
If that is the case, then I would not consider...

If that is the case, then I would not consider looking for DE, especially by cuffdiff, to be at all a valid means of determining how similar/dissimilar the samples are. Particularly if the samples...
Forum: RNA Sequencing 09-10-2013, 08:23 AM
Replies: 4
Views: 1,499
Posted By chadn737
Why is that bad? Depending on what the samples...

Why is that bad? Depending on what the samples are, I do not find that unusual at all.
Forum: General 09-09-2013, 11:17 AM
Replies: 27
Views: 7,817
Posted By chadn737
Has anyone here used a macbook air? I am really...

Has anyone here used a macbook air? I am really tempted to switch from my 15 inch macbook pro to a 13 inch air, move all my analysis to the server (which I really should do anyhow) and use a monitor...
Forum: Sanger/Dye Terminator 09-09-2013, 08:46 AM
Replies: 20
Views: 22,125
Posted By chadn737
It depends upon your institution/business. At the...

It depends upon your institution/business. At the Universities that I have worked at, there are core facilities and no shipping costs. It takes a day or so to get results, but per sample the cost is...
Forum: Sample Prep / Library Generation 09-05-2013, 09:43 AM
Replies: 4
Views: 5,796
Posted By chadn737
If you are worried about it, why not throw in a...

If you are worried about it, why not throw in a little RNase, let it work its magic for a while, and clean up your samples? You shouldn't loose much, particularly if you use a Phenol/Chlorophorm...
Forum: RNA Sequencing 08-29-2013, 12:07 PM
Replies: 11
Views: 9,656
Posted By chadn737
Then that is a difference between aligners, not...

Then that is a difference between aligners, not htseq-count vs RSEM. htseq-count does not align reads or determine their locations. That is done by whatever aligner is used prior to that. So an...
Forum: RNA Sequencing 08-29-2013, 11:40 AM
Replies: 11
Views: 9,656
Posted By chadn737
The "HTS also assigns some low counts to some...

The "HTS also assigns some low counts to some pseudogenes which RSEM seems to avoid doing" does not make sense to me given how htseq-count works, those reads assigned to pseudogenes would have to be...
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