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Forum: Bioinformatics 01-09-2016, 08:02 AM
Replies: 1
Views: 1,391
Posted By thickrick99
Question Amino Acid Sequence from Exome Data?

Hi Everyone,

I working on a project that requires an amino acid sequence of exome sequence data. My first approach was to use samtool's mpileup command to get a consensus sequence from the exome...
Forum: Bioinformatics 12-28-2015, 11:18 AM
Replies: 2
Views: 1,712
Posted By thickrick99
Thanks for the response! Both of these tools seem...

Thanks for the response! Both of these tools seem helpful, however do they output the sequence of the flanking region/altered amino acid sequence as well? I quickly looked through snpEff and Annovar...
Forum: Bioinformatics 12-18-2015, 03:26 PM
Replies: 2
Views: 1,712
Posted By thickrick99
Question Is SAMtools the right software for this project?

Hi Everyone,

Here is a brief summary of what I am trying to do with my project: Essentially, I want to find how a mutation in the mRNA sequence affects the amino acid sequence of a protein. I have...
Forum: Bioinformatics 08-26-2014, 02:28 AM
Replies: 1
Views: 1,315
Posted By thickrick99
I am still trying to figure this out however, I...

I am still trying to figure this out however, I don't know how to index the CuffGeneSet object. If there is now solution to my above question, then I guess my only option is to have multiple heat...
Forum: Bioinformatics 08-25-2014, 01:55 PM
Replies: 1
Views: 1,315
Posted By thickrick99
Question How to Filter Significant Genes??

Hi Everyone,

I am using cummeRbund to do some DE analysis and have 3 samples each having 5 biological replicates. Right now, the number of significant genes in the CuffGeneSet object is 548 with...
Forum: Bioinformatics 08-19-2014, 01:18 PM
Replies: 20
Views: 9,478
Posted By thickrick99
Sorry to bring back an old thread but has anyone...

Sorry to bring back an old thread but has anyone found a solution for this yet?? I posted in the RNA-seq forum and still have no replies but I am facing the same issue and can't seem to find a...
Forum: RNA Sequencing 08-18-2014, 11:34 AM
Replies: 1
Views: 2,529
Posted By thickrick99
I also tried this with a newer version of...

I also tried this with a newer version of cufflinks and it did not work.. still giving me the same error.
Forum: RNA Sequencing 08-18-2014, 07:45 AM
Replies: 1
Views: 2,529
Posted By thickrick99
Question Cuffmerge can't execute gtf_to_sam

Hi Everyone,

I am having some issues with cuff merge right now because it is giving me an error that it could not execute gtf_to_sam. I have seen other questions posted about this but couldn't...
Forum: RNA Sequencing 08-18-2014, 06:09 AM
Replies: 13
Views: 2,328
Posted By thickrick99
Ok thanks for your help Gordon. So I tried using...

Ok thanks for your help Gordon. So I tried using the t-test on the FPKM values but I realized that I can't do the test because of the 0 FPKM values. Is there an accepted way to get around this so...
Forum: RNA Sequencing 08-17-2014, 08:20 AM
Replies: 13
Views: 2,328
Posted By thickrick99
ok thanks Devon! So I have my count data, but how...

ok thanks Devon! So I have my count data, but how do I got about using the negative binomial model. I am not very familiar with these types of models (since I just started in this field very...
Forum: RNA Sequencing 08-17-2014, 06:28 AM
Replies: 13
Views: 2,328
Posted By thickrick99
So if I wanted to use more complicated tests with...

So if I wanted to use more complicated tests with poisson or negative binomial I would have to use the raw read count data right? Where do I access this information assuming I used top hat and then...
Forum: RNA Sequencing 08-17-2014, 04:59 AM
Replies: 13
Views: 2,328
Posted By thickrick99
Yeah that's what I was planning to do as well....

Yeah that's what I was planning to do as well. But I read online about other tests like poisson or negative binomial and I wasn't sure if these are better than using the T-test?
Forum: RNA Sequencing 08-16-2014, 01:33 PM
Replies: 13
Views: 2,328
Posted By thickrick99
I understand that I don't actually need a test...

I understand that I don't actually need a test statistic since programs like cuffdiff can do it for me. However, as part of the project I am working on, I need to program a test statistic with R in...
Forum: RNA Sequencing 08-16-2014, 01:04 PM
Replies: 13
Views: 2,328
Posted By thickrick99
Ok thanks for the advice! I haven't run cuffdiff...

Ok thanks for the advice! I haven't run cuffdiff yet but I will now. So what you're saying is, I can look for genes with similar expression in the .diff file and then look at the isoforms that have a...
Forum: RNA Sequencing 08-16-2014, 11:08 AM
Replies: 13
Views: 2,328
Posted By thickrick99
Question Advice for Statistics in Gene Expression??

Hi Everyone,

I am a beginner in RNA-seq and am working on a project dealing with differential gene expression. I am trying to compare the gene expression between two populations each having 2-5...
Forum: RNA Sequencing 08-12-2014, 07:55 PM
Replies: 1
Views: 2,516
Posted By thickrick99
Post Tophat Can't Find Bowtie2 Index!?!?!

Hi everyone,

So I am familiar with using tophat for alignment and I used it successfully a few weeks ago with the following command:

tophat -p 4 –G...
Forum: RNA Sequencing 08-12-2014, 12:10 PM
Replies: 2
Views: 1,882
Posted By thickrick99
Post Advice Needed on Tuxedo Suite

Hi Everyone,

I am working on a project with two groups (A & B) each containing 5 samples. Within each sample I have two RNA-seq FASTQ reads which I downloaded. So as of now, I am planning to run...
Forum: RNA Sequencing 08-11-2014, 06:34 AM
Replies: 0
Views: 938
Posted By thickrick99
Question Where to get Population RNA-seq Data??

Hi Everyone,

I was wondering if anybody knows databases where I can get population specific RNA-seq data. I know that Geuvadis has a collection of RNA-seq data with GBR, FIN, TSI, etc. but these...
Forum: RNA Sequencing 07-04-2014, 11:17 AM
Replies: 5
Views: 3,279
Posted By thickrick99
Alright Cool! Yeah I heard that GATK is useful in...

Alright Cool! Yeah I heard that GATK is useful in SNP calling so I will definitely read through the protocol.

Thanks Again!
Forum: RNA Sequencing 07-04-2014, 11:01 AM
Replies: 5
Views: 3,279
Posted By thickrick99
Thanks blancha for your advice especially on the...

Thanks blancha for your advice especially on the FPKM values! Yeah it makes sense to keep them since I can identify genes that are not expressed.

Sorry for the really broad questions. Essentially...
Forum: RNA Sequencing 07-04-2014, 08:30 AM
Replies: 5
Views: 3,279
Posted By thickrick99
Question What do I do with output files from tophat/cufflinks

Hi I am a beginner with RNA-sequencing and I used tophat to align RNA-seq reads from geuvadis to hg19 from UCSC. In tophat, I provided the reference transcript and then used the accepted_hits.bam...
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