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Forum: Bioinformatics 12-21-2014, 01:30 AM
Replies: 1
Views: 1,562
Posted By shocker8786
GATK IndelRealigner error

Hello,

I'm attempting to use GATK 2.3-9-ge5ebf34 to re-align some RNA-seq datasets. Below is the code I'm using.

java -Xms16g -jar ~/bin/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -T...
Forum: Bioinformatics 05-21-2014, 01:59 AM
Replies: 3
Views: 1,499
Posted By shocker8786
I downloaded the patch and everything seems to be...

I downloaded the patch and everything seems to be running properly now. Thank you very much!
Forum: Bioinformatics 05-20-2014, 03:01 AM
Replies: 3
Views: 1,499
Posted By shocker8786
STAR aligner issue

I am trying to align some paired end RNAseq data using STAR (version 2.3.0e), but I'm having an issue with the alignment. My code is:

$HOME/bin/STAR_2.3.0e/STAR --genomeDir...
Forum: Bioinformatics 04-21-2014, 05:24 AM
Replies: 13
Views: 3,358
Posted By shocker8786
Yes, that seems to have solved the problem. Thank...

Yes, that seems to have solved the problem. Thank you very much!
Forum: Bioinformatics 04-19-2014, 12:55 PM
Replies: 13
Views: 3,358
Posted By shocker8786
Thanks, I think we're getting closer. I received...

Thanks, I think we're getting closer. I received a different error message this time.

>...
Forum: Bioinformatics 04-19-2014, 08:50 AM
Replies: 13
Views: 3,358
Posted By shocker8786
Yeah sorry, I guess that wasn't clear. I've gone...

Yeah sorry, I guess that wasn't clear. I've gone through the vignette with the test dataset, and am now using my own dataset. Here are the results from the requested commands.

sessionInfo()
R...
Forum: Bioinformatics 04-16-2014, 06:19 AM
Replies: 13
Views: 3,358
Posted By shocker8786
Issue with BiSeq for DMR analysis

I'm hoping someone has experience using the BiSeq package in R. I'm going through the "An Introduction to BiSeq" pdf available at the following website:
...
Forum: Bioinformatics 03-31-2014, 02:01 AM
Replies: 3
Views: 2,323
Posted By shocker8786
Cufflinks 2.2.0 installation issue

I want to use the new cuffquant and cuffnorm features of cufflinks 2.2.0, so I removed my 2.1.1 version of cufflinks and downloaded the source code for version 2.2.0. However, after installation, I...
Forum: Bioinformatics 03-18-2014, 01:27 AM
Replies: 92
Views: 36,042
Posted By shocker8786
Thank you very much for that explanation, this is...

Thank you very much for that explanation, this is starting to make more sense to me now. I will make the necessary changes and retry. Thanks again!
Forum: Bioinformatics 03-17-2014, 02:11 AM
Replies: 92
Views: 36,042
Posted By shocker8786
I retried the code and was still not successful...

I retried the code and was still not successful with one of my datasets. I am sure that the code I am using is the same for both datasets (I have been copying and pasting the code for both datasets)....
Forum: Bioinformatics 03-15-2014, 05:17 AM
Replies: 92
Views: 36,042
Posted By shocker8786
Thank you for your help. I have 2 data sets that...

Thank you for your help. I have 2 data sets that I am trying to perform this analysis on (all pig), and I was indeed able to produce the results files as expected by changing those lines of code for...
Forum: Bioinformatics 03-14-2014, 01:29 AM
Replies: 92
Views: 36,042
Posted By shocker8786
I think you are right, but I'm not sure how...

I think you are right, but I'm not sure how exactly to download the pathway data files. I thought the step you told me to change (below) would download the package I need, but it fails:
...
Forum: Bioinformatics 03-13-2014, 01:26 AM
Replies: 92
Views: 36,042
Posted By shocker8786
Thanks for your reply, and for informing me about...

Thanks for your reply, and for informing me about the org="Ss" command. Unfortunately I am still unable to make it through the workflow without error. Below is my code and final output. Do you see...
Forum: Bioinformatics 03-12-2014, 07:32 AM
Replies: 92
Views: 36,042
Posted By shocker8786
changing range(exp.fc) to range(cuff.fc) results...

changing range(exp.fc) to range(cuff.fc) results in the following result printed by R:
[1] -Inf Inf

So is this a typo in the RNAseq workflow, or am I already supposed to have exp.fc defined? I'm...
Forum: Bioinformatics 03-12-2014, 07:02 AM
Replies: 92
Views: 36,042
Posted By shocker8786
I have a question about using GAGE with data from...

I have a question about using GAGE with data from cufflinks, as described in the RNA-Seq workflow tutorial. I have RNAseq data from pigs that was aligned using Tophat and analyzed for DEGs using...
Forum: Bioinformatics 02-19-2014, 10:10 PM
Replies: 2
Views: 1,276
Posted By shocker8786
As I said in the original post, I sorted by read...

As I said in the original post, I sorted by read name. However I know the unpaired reads have the /1 and /2 read name endings, so maybe that could be the issue?
Forum: Bioinformatics 02-19-2014, 04:20 AM
Replies: 2
Views: 1,276
Posted By shocker8786
Error when using HTSeq count

I used Tophat to produce a bam file from paired end RNAseq data, as well as unpaired reads that were retained after trimming. I then sorted by read name and converted the bam to a sam file. When I...
Forum: Bioinformatics 02-05-2014, 01:40 AM
Replies: 6
Views: 3,469
Posted By shocker8786
Thank you very much for your response, that makes...

Thank you very much for your response, that makes a lot of sense.
Forum: Bioinformatics 02-04-2014, 11:55 PM
Replies: 6
Views: 3,469
Posted By shocker8786
Align paired and unpaired reads with Tophat

I have a stranded PE RNAseq data set that I want to align with tophat using the --library-type fr-firststrand option. After adaptor trimming I end up with my 4 files:

paired_1
paired_2...
Forum: Bioinformatics 01-22-2014, 06:39 AM
Replies: 1
Views: 1,222
Posted By shocker8786
remove overlapping PE reads RRBS

I'm working with PE RRBS data. The library fragment size is 40-220bp, and the reads are 50bp PE reads. Because of this, there are a significant amount of regions in which the PE reads overlap. I'm...
Forum: Bioinformatics 11-25-2013, 07:11 AM
Replies: 0
Views: 900
Posted By shocker8786
Determine CpG Island coverage

I'm working with some Reduced Representation Bisulfite Sequenced datasets. After aligning the reads to the reference genome (Sus Scrofa), I want to determine the number (percent) of CpG islands I...
Forum: Bioinformatics 10-14-2013, 05:59 AM
Replies: 6
Views: 4,434
Posted By shocker8786
Thanks. I do not have administrative privilages,...

Thanks. I do not have administrative privilages, so I'm unable to increase the maximum number of open files (16384).

How would I go about reducing the number of threads used?
Forum: Bioinformatics 10-11-2013, 11:41 PM
Replies: 6
Views: 4,434
Posted By shocker8786
Thanks for your reply. I tried extending the...

Thanks for your reply. I tried extending the library using those options in the link, but I still have the same error. I checked the @INC paths and the path to the Scalar/Util.pm...
Forum: Bioinformatics 10-11-2013, 07:09 AM
Replies: 6
Views: 4,434
Posted By shocker8786
Problem running BSmooth

I'm trying to use BSmooth to align RRBS reads. I keep getting an error after the program processes 70000 reads:

Processed 65000 reads (19.171 knt/s, 28.502% align in 1 orientation, 48.277% in...
Forum: Bioinformatics 10-09-2013, 04:55 AM
Replies: 2
Views: 1,818
Posted By shocker8786
Trim Galore output issue

I have both RRBS and RNAseq datasets that I'm trying to filter for quality and trim adaptors using Trim Galore. When I run it on the RRBS fq files using the --RRBS option, the resulting fq output...
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