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Bridgecrest Bioinformatics

Monday, November 26, 2012. Comparing Lists Using a Shell Script. Here is a script I've used enough times that I thought other people might find it useful as well:. Https:/ gist.github.com/4151008. If you have 1, 2, or 3 lists (one item per line), it will print out the counts for each of the sections of a Venn diagram. Lists do not need to be sorted. Let me know if you see any problems or have any improvements for it. Wednesday, October 31, 2012. Gene Names Are Broken. Of Names Length of Name. There is to...

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Bridgecrest Bioinformatics | bridgecrest.blogspot.com Reviews

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Monday, November 26, 2012. Comparing Lists Using a Shell Script. Here is a script I've used enough times that I thought other people might find it useful as well:. Https:/ gist.github.com/4151008. If you have 1, 2, or 3 lists (one item per line), it will print out the counts for each of the sections of a Venn diagram. Lists do not need to be sorted. Let me know if you see any problems or have any improvements for it. Wednesday, October 31, 2012. Gene Names Are Broken. Of Names Length of Name. There is to...

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Bridgecrest Bioinformatics | bridgecrest.blogspot.com Reviews

https://bridgecrest.blogspot.com

Monday, November 26, 2012. Comparing Lists Using a Shell Script. Here is a script I've used enough times that I thought other people might find it useful as well:. Https:/ gist.github.com/4151008. If you have 1, 2, or 3 lists (one item per line), it will print out the counts for each of the sections of a Venn diagram. Lists do not need to be sorted. Let me know if you see any problems or have any improvements for it. Wednesday, October 31, 2012. Gene Names Are Broken. Of Names Length of Name. There is to...

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bridgecrest.blogspot.com

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Bridgecrest Bioinformatics: October 2012

http://bridgecrest.blogspot.com/2012_10_01_archive.html

Wednesday, October 31, 2012. Gene Names Are Broken. For some interesting ones, such as pokemon or sonic hedgehog - the approved gene name). Now, I'm not the first to notice this, and there is actually a committee called the HUGO Gene Nomenclature Committee. HGNC) to "assign unique gene symbols and names to over 33,500 human loci". Too bad some of these symbols are utterly useless. The symbols may be unique with respect to other gene symbols, but they are far from unique and distinguishing. Often times an...

2

Bridgecrest Bioinformatics

http://bridgecrest.blogspot.com/2012/02/many-times-i-find-neat-or-useful-1-or-2.html

Sunday, February 5, 2012. Many times I find a neat or useful 1 or 2 line unix command, but I end up having to look it up again and again. For this post, I plan to jot down a few commands that I think are helpful - I'll keep adding more as I come across them. Reverse Complement a DNA sequence. Let's say you have a file named sequence.txt that looks like this . . . You can reverse complement it by doing this. Tr -d ' n' output.fa rev tr 'ACGTacgt' 'TGCAtgca' fold -w 80 output.txt. Find xargs grep whatever.

3

Bridgecrest Bioinformatics: September 2011

http://bridgecrest.blogspot.com/2011_09_01_archive.html

Sunday, September 4, 2011. This week I decided to try the transformations and plots out on real data and see what I get. I used the data from the Marioni. Paper that discusses reproducibility among technical replicates. The data consists of technical replicates of both liver and kidney at various concentrations. I used their available aligned data. And counted (using BEDTools. The number of reads that fell within each gene from the Hg18 knownGene. Here I transform the data using the Anscombe Transform, w...

4

Bridgecrest Bioinformatics: August 2011

http://bridgecrest.blogspot.com/2011_08_01_archive.html

Sunday, August 28, 2011. The Use of Log-Log plots to show technical reproducibility of NGS data. Links to Pictures of Log-Log RPKM plots between Technical Replicates. My guess is that the RPKM values are logged because that is what is done to microarray expression values. A common plot that is used to compare two microarray samples is the MA plot. If the data looked homoscedastic after logging the values, then the data would have a log-normal. Variance Stabilization for Count data. This will magically ma...

5

Bridgecrest Bioinformatics

http://bridgecrest.blogspot.com/2011/09/technical-replicates-continued-last.html

Sunday, September 4, 2011. This week I decided to try the transformations and plots out on real data and see what I get. I used the data from the Marioni. Paper that discusses reproducibility among technical replicates. The data consists of technical replicates of both liver and kidney at various concentrations. I used their available aligned data. And counted (using BEDTools. The number of reads that fell within each gene from the Hg18 knownGene. Here I transform the data using the Anscombe Transform, w...

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Bridgecrest Bioinformatics

Monday, November 26, 2012. Comparing Lists Using a Shell Script. Here is a script I've used enough times that I thought other people might find it useful as well:. Https:/ gist.github.com/4151008. If you have 1, 2, or 3 lists (one item per line), it will print out the counts for each of the sections of a Venn diagram. Lists do not need to be sorted. Let me know if you see any problems or have any improvements for it. Wednesday, October 31, 2012. Gene Names Are Broken. Of Names Length of Name. There is to...

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