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Search: Posts Made By: blakeoft
Forum: Bioinformatics 06-09-2015, 10:24 AM
Replies: 22
Views: 21,122
Posted By blakeoft
resara, I picked 50 base pairs as an...

resara,

I picked 50 base pairs as an example. However, I don't think that 0-indexing or otherwise will affect how much you want to shift the reads. For example, 0 -> 50 vs 1 -> 51 is is still a...
Forum: Bioinformatics 06-09-2015, 05:55 AM
Replies: 22
Views: 21,122
Posted By blakeoft
It looks like you just need to have Python...

It looks like you just need to have Python installed, so you won't need to do any kind of Python programming. Check out the INTALL.rst file in the macs2 tarball for information on what you need to...
Forum: Bioinformatics 06-02-2015, 07:06 AM
Replies: 22
Views: 21,122
Posted By blakeoft
You can use bamToBed from bedtools to convert...

You can use bamToBed from bedtools to convert from bam to bed format as you have mentioned. It's quite easy to adjust the start and end site of reads in bed format. I'm not an awk master, so there's...
Forum: Bioinformatics 05-22-2015, 07:42 AM
Replies: 3
Views: 1,223
Posted By blakeoft
If I recall correctly, I wasn't able to actually...

If I recall correctly, I wasn't able to actually find this in the TopHat documentation, but take a look at this discussion (https://www.biostars.org/p/69773/). According to the top answer, the...
Forum: Bioinformatics 05-21-2015, 09:54 AM
Replies: 1
Views: 3,252
Posted By blakeoft
I think the problem is that your modcombat matrix...

I think the problem is that your modcombat matrix doesn't have the right dimensions. When you run

modcombat = model.matrix(~1, data=dat)

you'll get an n by 1 matrix with each entry equal to 1,...
Forum: General 05-19-2015, 11:16 AM
Replies: 2
Views: 929
Posted By blakeoft
This reminds me of Sonic Hedgehog and Pikachurin.

This reminds me of Sonic Hedgehog and Pikachurin.
Forum: Bioinformatics 05-08-2015, 10:35 AM
Replies: 15
Views: 4,228
Posted By blakeoft
The help file of the version of cummeRbund that...

The help file of the version of cummeRbund that I'm using says that the labels parameter isn't implemented yet, in other words it doesn't do anything yet. Besides, the plot would probably be...
Forum: Bioinformatics 05-05-2015, 11:27 AM
Replies: 15
Views: 4,228
Posted By blakeoft
After reading in some of my old cufflinks data,...

After reading in some of my old cufflinks data, I've realized that my second post in this discussion has some incorrect code. Please plot these two figures for comparison:

csScatter(genes(cuff),...
Forum: Bioinformatics 05-05-2015, 04:53 AM
Replies: 15
Views: 4,228
Posted By blakeoft
I saw the prefix "TRAP", and it made me think of...

I saw the prefix "TRAP", and it made me think of Trapnell, as in Cole Trapnell. This is why I was curious if you were working with some kind of sample data set or something.

Your code should be...
Forum: Bioinformatics 05-04-2015, 10:27 AM
Replies: 15
Views: 4,228
Posted By blakeoft
I have a couple questions for you. Are you...

I have a couple questions for you. Are you following some sort of published analysis? Also, does each row of samples(cuff) have a column in m? In other words, what does all(colnames(m) %in%...
Forum: Bioinformatics 05-01-2015, 08:47 AM
Replies: 15
Views: 4,228
Posted By blakeoft
Marcos, Did you ever sort this out? I would...

Marcos,

Did you ever sort this out? I would double check that you're supplying the right vectors to cor(). It might also have to do with how csScatter doesn't plot all of the data points. It's...
Forum: Bioinformatics 04-27-2015, 10:51 AM
Replies: 15
Views: 4,228
Posted By blakeoft
Thanks for the tip cmbetts. It looks like you...

Thanks for the tip cmbetts. It looks like you want to execute
m <- fpkmMatrix(genes(cuffdiff_output))
cor(m[, 1], m[, 2]) # or whatever columns you need

Keep in mind that csScatter() might...
Forum: Bioinformatics 04-27-2015, 04:53 AM
Replies: 15
Views: 4,228
Posted By blakeoft
You might have to use cor(), a base R function....

You might have to use cor(), a base R function. However, I don't know exactly how to subset a CuffData object so that you get the proper input for cor().
Forum: RNA Sequencing 04-02-2015, 10:15 AM
Replies: 22
Views: 28,102
Posted By blakeoft
Gonza, There are several different types of...

Gonza,

There are several different types of gene identifiers. If you have a vector of gene names, you could take them to Ensembl's Biomart (http://www.ensembl.org/biomart/martview). There's also a...
Forum: Bioinformatics 12-29-2014, 07:05 AM
Replies: 2
Views: 2,485
Posted By blakeoft
Your formula for RPKM is wrong. Replace read...

Your formula for RPKM is wrong. Replace read length with transcript length. So you'll need to calculate:

(number of reads mapped to a transcript) / (totat number of reads X transcript length) X...
Forum: Bioinformatics 12-17-2014, 11:22 AM
Replies: 4
Views: 2,005
Posted By blakeoft
Are you sure that the fastq files are in that...

Are you sure that the fastq files are in that directory?
Forum: Bioinformatics 12-16-2014, 05:17 AM
Replies: 8
Views: 2,357
Posted By blakeoft
I'm still able to access the courseware, but I...

I'm still able to access the courseware, but I can't find it archived by searching. It looks like it will be offered again next year with a different format. Search for PH525.
Forum: Bioinformatics 12-04-2014, 09:50 AM
Replies: 5
Views: 3,494
Posted By blakeoft
bsp017, Have you looked into RCircos? I too...

bsp017,

Have you looked into RCircos? I too have struggled with Circos in the past (so much so that I never managed to do anything meaningful), but I think RCircos might be a little easier to use....
Forum: RNA Sequencing 11-28-2014, 12:28 PM
Replies: 22
Views: 28,102
Posted By blakeoft
I'm not able to give you the best answer since...

I'm not able to give you the best answer since I'm not at my work station.

Have a look at this link though. Please let me know if you're still having trouble after reading.
...
Forum: Bioinformatics 11-26-2014, 10:22 AM
Replies: 1
Views: 2,047
Posted By blakeoft
I assume that the QUAL field is dependent on...

I assume that the QUAL field is dependent on quality scores of base calls of the reads that map to a particular locus. Of course it really depends on what software made the VCF file, but I imagine...
Forum: RNA Sequencing 11-26-2014, 08:59 AM
Replies: 22
Views: 28,102
Posted By blakeoft
Gonza, Sorry for the late reply. Can you...

Gonza,

Sorry for the late reply. Can you explain your data a little more? You want to add error bars, but that usually means that you have upper and lower bounds. At first it looks like you want...
Forum: RNA Sequencing 11-14-2014, 04:24 AM
Replies: 16
Views: 11,055
Posted By blakeoft
Gonza, Have you looked at line 1390 of the...

Gonza,

Have you looked at line 1390 of the genes.fpkm_tracking file?
Forum: Bioinformatics 11-11-2014, 11:56 AM
Replies: 6
Views: 2,055
Posted By blakeoft
Thank you, jwfoley. I've thought about what...

Thank you, jwfoley. I've thought about what you've said and it makes a good amount of sense. I'm using ggplot2 in R to make these visualizations. It may not be the best approach, but I'm most...
Forum: Bioinformatics 11-10-2014, 10:28 AM
Replies: 5
Views: 2,198
Posted By blakeoft
Can you download the latest versions of tophat...

Can you download the latest versions of tophat and bowtie2 to your home directory? That would be a pretty easy fix, and you'd have the latest version of the software too.
Forum: Bioinformatics 11-04-2014, 07:49 AM
Replies: 3
Views: 1,439
Posted By blakeoft
The number of reads is the ((Rz *...

The number of reads is the ((Rz * Length_of_the_transcript) / read_length) part.

I'll try and explain.

Let N be the number of bases being considered, i.e. the length of the transcript. Let c_i...
Showing results 1 to 25 of 79

 


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