Forum: Bioinformatics
02-06-2014, 04:06 PM
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Replies: 1
Views: 1,558
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...
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Forum: Bioinformatics
01-31-2014, 11:52 AM
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Replies: 11
Views: 8,284
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...
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Forum: Bioinformatics
01-31-2014, 08:53 AM
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Replies: 11
Views: 8,284
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Forum: Bioinformatics
01-21-2014, 10:03 AM
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Replies: 3
Views: 2,360
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Forum: RNA Sequencing
10-21-2013, 08:27 AM
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Replies: 6
Views: 1,714
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".
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Forum: RNA Sequencing
10-10-2013, 09:44 AM
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Replies: 9
Views: 10,717
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Forum: Illumina/Solexa
10-09-2013, 02:25 PM
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Replies: 5
Views: 2,812
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Forum: RNA Sequencing
10-04-2013, 06:37 PM
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Replies: 1
Views: 2,758
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Forum: RNA Sequencing
10-02-2013, 08:09 AM
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Replies: 9
Views: 5,813
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Forum: 454 Pyrosequencing
10-01-2013, 08:10 PM
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Replies: 6
Views: 4,439
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...
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Forum: RNA Sequencing
09-30-2013, 08:51 PM
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Replies: 7
Views: 7,591
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.
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Forum: Bioinformatics
09-24-2013, 04:49 PM
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Replies: 26
Views: 16,167
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...
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Forum: RNA Sequencing
09-23-2013, 03:12 PM
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Replies: 2
Views: 1,484
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Forum: RNA Sequencing
09-22-2013, 02:18 PM
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Replies: 2
Views: 2,213
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Forum: Bioinformatics
09-22-2013, 12:17 PM
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Replies: 4
Views: 2,992
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Forum: Sample Prep / Library Generation
09-20-2013, 06:54 PM
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Replies: 4
Views: 2,291
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...
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Forum: Bioinformatics
09-11-2013, 09:18 AM
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Replies: 2
Views: 2,691
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Forum: General
09-10-2013, 10:45 AM
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Replies: 27
Views: 9,749
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Forum: RNA Sequencing
09-10-2013, 10:35 AM
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Replies: 4
Views: 1,920
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...
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Forum: RNA Sequencing
09-10-2013, 09:23 AM
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Replies: 4
Views: 1,920
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Forum: General
09-09-2013, 12:17 PM
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Replies: 27
Views: 9,749
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...
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Forum: Sanger/Dye Terminator
09-09-2013, 09:46 AM
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Replies: 20
Views: 24,468
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Forum: Sample Prep / Library Generation
09-05-2013, 10:43 AM
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Replies: 4
Views: 6,613
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Forum: RNA Sequencing
08-29-2013, 01:07 PM
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Replies: 11
Views: 13,173
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Forum: RNA Sequencing
08-29-2013, 12:40 PM
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Replies: 11
Views: 13,173
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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