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Search: Posts Made By: mbblack
Forum: Bioinformatics 03-22-2017, 05:43 AM
Replies: 2
Views: 1,585
Posted By mbblack
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...
Forum: Bioinformatics 10-25-2016, 09:51 AM
Replies: 6
Views: 1,566
Posted By mbblack
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...
Forum: Bioinformatics 10-25-2016, 09:41 AM
Replies: 2
Views: 799
Posted By mbblack
Have you simply gone to...

Have you simply gone to http://www.genome.jp/kegg/ and looked at the information there?
Forum: Bioinformatics 05-02-2016, 11:14 AM
Replies: 2
Views: 987
Posted By mbblack
Directly quoted from the RefSeq FAQ...

Directly quoted from the RefSeq FAQ (http://www.ncbi.nlm.nih.gov/books/NBK50679/)
Forum: RNA Sequencing 02-02-2016, 07:43 AM
Replies: 5
Views: 5,156
Posted By mbblack
What flavor of Linux are you running? You may be...

What flavor of Linux are you running? You may be able to simply use your system's package manager to do this.

For example, with CentOS 7 and epel repository installed, a simple:

sudo yum...
Forum: Bioinformatics 08-05-2015, 05:12 AM
Replies: 1
Views: 493
Posted By mbblack
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...
Forum: Oxford Nanopore 05-18-2015, 01:02 PM
Replies: 10
Views: 3,551
Posted By mbblack
:) The sequencing world is always very different...

:) The sequencing world is always very different every year or two.
Forum: RNA Sequencing 05-08-2015, 08:54 AM
Replies: 2
Views: 869
Posted By mbblack
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...
Forum: Bioinformatics 05-08-2015, 06:01 AM
Replies: 9
Views: 1,148
Posted By mbblack
Perhaps average absolute expression levels for a...

Perhaps average absolute expression levels for a given wild type tissue may behave that way. But you would not be able to address that question by sequencing whole cell mRNA.

Honestly, I'd be...
Forum: Bioinformatics 05-07-2015, 10:56 AM
Replies: 9
Views: 1,148
Posted By mbblack
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...
Forum: Bioinformatics 05-07-2015, 09:39 AM
Replies: 9
Views: 1,148
Posted By mbblack
Well, there are no such things as truly universal...

Well, there are no such things as truly universal housekeeping genes. For any gene that one person has found useful as a housekeeping gene, you can almost certianly find an example where it is...
Forum: RNA Sequencing 04-21-2015, 08:46 AM
Replies: 3
Views: 2,068
Posted By mbblack
chariko - have a look through this thread as it...

chariko - have a look through this thread as it should already give you the answer to your question - http://seqanswers.com/forums/showthread.php?t=45526
Forum: RNA Sequencing 04-21-2015, 08:35 AM
Replies: 3
Views: 1,435
Posted By mbblack
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...
Forum: RNA Sequencing 04-13-2015, 05:45 AM
Replies: 2
Views: 1,543
Posted By mbblack
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...
Forum: RNA Sequencing 03-05-2015, 06:51 AM
Replies: 2
Views: 1,237
Posted By mbblack
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...
Forum: Bioinformatics 02-12-2015, 11:04 AM
Replies: 15
Views: 2,409
Posted By mbblack
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...
Forum: General 02-10-2015, 09:13 AM
Replies: 6
Views: 7,616
Posted By mbblack
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...
Forum: General 02-10-2015, 06:58 AM
Replies: 6
Views: 7,616
Posted By mbblack
If in any doubt, just open the file in any ASCII...

If in any doubt, just open the file in any ASCII text editor and look at it. The FASTA file format is about as simple a text format as you can get, and easily checked:
...
Forum: Illumina/Solexa 02-05-2015, 11:48 AM
Replies: 8
Views: 2,543
Posted By mbblack
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...
Forum: Bioinformatics 02-05-2015, 07:36 AM
Replies: 9
Views: 3,936
Posted By mbblack
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...
Forum: RNA Sequencing 01-30-2015, 06:02 AM
Replies: 2
Views: 995
Posted By mbblack
Generally speaking, what people are comfortable...

Generally speaking, what people are comfortable with for DGE is nowhere near what is ideal for high confidence SNP calling. Illumina has a 2010 white paper looking at depth of coverage and SNP...
Forum: Bioinformatics 11-12-2014, 12:45 PM
Replies: 10
Views: 3,377
Posted By mbblack
I just don't know anyone who would be comfortable...

I just don't know anyone who would be comfortable using lack of detection in an RNA-seq experiment as confirmation of a successful knockout. The gold standard still seems to clearly be demonstrating...
Forum: Bioinformatics 11-12-2014, 12:13 PM
Replies: 10
Views: 3,377
Posted By mbblack
Or, that feature is truly not expressed in that...

Or, that feature is truly not expressed in that sample or tissue or under those conditions. But you have no way of distinguishing between the two situations. And you certainly cannot say anything...
Forum: Bioinformatics 11-12-2014, 12:10 PM
Replies: 10
Views: 3,377
Posted By mbblack
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...
Forum: RNA Sequencing 11-12-2014, 12:05 PM
Replies: 4
Views: 2,660
Posted By mbblack
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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