Forum: Bioinformatics
03-22-2017, 05:43 AM
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Replies: 2
Views: 3,739
As mentioned, the BAM files you download were...
As mentioned, the BAM files you download were prepared and uploaded by the submitter (FASTQ, while supported, is not a preferred format for SRA and is accepted as reference sequences for the aligned...
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Forum: Bioinformatics
10-25-2016, 09:51 AM
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Replies: 6
Views: 3,298
The public consortium human genome reference...
The public consortium human genome reference sequence is explicitly a consensus sequence (actually stated as such in the 2001 Science paper) of five individual humans used to produce the plasmid...
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Forum: Bioinformatics
10-25-2016, 09:41 AM
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Replies: 2
Views: 1,254
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Forum: Bioinformatics
05-02-2016, 11:14 AM
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Replies: 2
Views: 1,378
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Forum: RNA Sequencing
02-02-2016, 07:43 AM
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Replies: 5
Views: 7,506
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Forum: Bioinformatics
08-05-2015, 05:12 AM
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Replies: 1
Views: 800
In general, Bayes Factors are a bit like...
In general, Bayes Factors are a bit like interpreting a p-value and the choice of cutoff for "significance" is arbitrary. The Jeffrey's scale is one widely used suggested scaling of significance...
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Forum: Oxford Nanopore
05-18-2015, 01:02 PM
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Replies: 10
Views: 4,419
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Forum: RNA Sequencing
05-08-2015, 08:54 AM
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Replies: 2
Views: 1,180
You mean the same GO terms in both the...
You mean the same GO terms in both the up-regulated and the down-regulated group? If so, sure that's highly possible. Remember that individual gene differential expression does not necessarily tell...
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Forum: Bioinformatics
05-08-2015, 06:01 AM
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Replies: 9
Views: 1,619
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Forum: Bioinformatics
05-07-2015, 10:56 AM
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Replies: 9
Views: 1,619
Yes, I've done some comparative studies of...
Yes, I've done some comparative studies of multiple tissues from the same animals (eg. rodent liver & lung from inhalation studies) and one can get near completely opposite differential expression of...
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Forum: Bioinformatics
05-07-2015, 09:39 AM
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Replies: 9
Views: 1,619
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Forum: RNA Sequencing
04-21-2015, 08:46 AM
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Replies: 3
Views: 3,353
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Forum: RNA Sequencing
04-21-2015, 08:35 AM
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Replies: 3
Views: 1,925
A p-value tells you something about an...
A p-value tells you something about an observation relative to a distribution of possible data. That means you require a mean and some knowledge of the variance about that mean. Neither can be...
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Forum: RNA Sequencing
04-13-2015, 05:45 AM
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Replies: 2
Views: 2,131
There are no universal housekeeping genes. ...
There are no universal housekeeping genes. Housekeeping genes need to be determined on a case by case basis. GAPDH can indeed be differentially expressed under any number of conditions. GAPDH has...
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Forum: RNA Sequencing
03-05-2015, 06:51 AM
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Replies: 2
Views: 2,187
Have a look at this statisticians discussion of...
Have a look at this statisticians discussion of replication with cell lines (since yes, conventional "biological" replication is not truly possible) - http://labstats.net/articles/cell_culture_n.html...
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Forum: Bioinformatics
02-12-2015, 11:04 AM
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Replies: 15
Views: 3,490
Depending on what you are looking for and your...
Depending on what you are looking for and your stringency requirements, could you switch to BLAT instead? Maybe adopt a tiered approach of a first pass with BLAT to reduce the search space, then...
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Forum: General
02-10-2015, 09:13 AM
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Replies: 6
Views: 15,179
Yes, I wasn't specifically thinking of the size...
Yes, I wasn't specifically thinking of the size of the specific file in question, but my point was that if you simply look at the first few lines of any text file you'd know whether it was in FASTA...
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Forum: General
02-10-2015, 06:58 AM
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Replies: 6
Views: 15,179
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Forum: Illumina/Solexa
02-05-2015, 11:48 AM
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Replies: 8
Views: 3,628
Note that regardless of depth of coverage, you...
Note that regardless of depth of coverage, you may well not be able to "confirm" some array results with an independent RNA-seq experiment. Just because you detect any given gene as significantly...
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Forum: Bioinformatics
02-05-2015, 07:36 AM
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Replies: 9
Views: 5,818
One advantage of starting from raw data and...
One advantage of starting from raw data and re-normalizing and analyzing yourself is that you can investigate the various original data sets for any potential bias in library size and signal...
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Forum: RNA Sequencing
01-30-2015, 06:02 AM
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Replies: 2
Views: 1,290
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Forum: Bioinformatics
11-12-2014, 12:45 PM
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Replies: 10
Views: 5,226
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Forum: Bioinformatics
11-12-2014, 12:13 PM
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Replies: 10
Views: 5,226
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Forum: Bioinformatics
11-12-2014, 12:10 PM
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Replies: 10
Views: 5,226
If you have independently confirmed that your...
If you have independently confirmed that your knockout truly has eliminated expression of the gene in your system, then of course that is a different situation. But I would not take the count of...
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Forum: RNA Sequencing
11-12-2014, 12:05 PM
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Replies: 4
Views: 3,383
Did you select differentially expressed genes...
Did you select differentially expressed genes solely by a statistical threshold? What if you simultaneously add a fold change threshold as well - do you get more consistent lists? You can look at...
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