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Forum: RNA Sequencing 09-20-2012, 12:05 PM
Replies: 3
Views: 3,933
Posted By Aholton
Bump having this problem too

Bump having this problem too
Forum: RNA Sequencing 09-04-2012, 12:19 PM
Replies: 3
Views: 1,020
Posted By Aholton
Running Python

Ok I can't seem to get the python program to run, I've moved the file over to our server and tried to run it using the command given -
"cat file.gb | gb2gtf.py > file.gtf"
by inserting my files...
Forum: RNA Sequencing 09-04-2012, 11:16 AM
Replies: 3
Views: 1,020
Posted By Aholton
Thank you very much! I'm starting the process...

Thank you very much! I'm starting the process now.
Forum: RNA Sequencing 08-31-2012, 01:53 PM
Replies: 3
Views: 1,020
Posted By Aholton
Building a GTF file

How would I go about building a GTF file from either the FASTA file or from this infromation (http://www.ncbi.nlm.nih.gov/nuccore/JN012242.1)
Forum: RNA Sequencing 08-31-2012, 12:20 PM
Replies: 0
Views: 752
Posted By Aholton
Tophat/Cuffdiff Transmembrane Proteins

Is it possible to have Tophat/Cuffdiff show only Transmembrane domain containing proteins? Thanks for the help!
Forum: RNA Sequencing 08-31-2012, 12:18 PM
Replies: 5
Views: 7,978
Posted By Aholton
Ok thank you so much! That makes much more sense...

Ok thank you so much! That makes much more sense now
Forum: RNA Sequencing 08-30-2012, 11:41 AM
Replies: 5
Views: 7,978
Posted By Aholton
Bump, still having the reoccuring problem.

Bump, still having the reoccuring problem.
Forum: RNA Sequencing 08-23-2012, 12:38 PM
Replies: 5
Views: 7,978
Posted By Aholton
Ok just checked and my CuffDiff output file...

Ok just checked and my CuffDiff output file gene_exp.diff is showing the first three columns as the same thing instead of showing me the geneid and gene so I'm assuming something is definitely wrong...
Forum: RNA Sequencing 08-23-2012, 12:02 PM
Replies: 5
Views: 7,978
Posted By Aholton
Post Tophat building Bowtie index from gtf file

Not really a problem, as much as an inquiry. When I run Tophat it tells me that it is building a Bowtie index from my .gtf file I've supplied. However, I already supplied a Bowtie2 index in the...
Forum: RNA Sequencing 07-30-2012, 11:33 AM
Replies: 17
Views: 7,706
Posted By Aholton
No problem! If you need anything else feel free...

No problem! If you need anything else feel free to private message me
Forum: RNA Sequencing 07-27-2012, 06:05 AM
Replies: 17
Views: 7,706
Posted By Aholton
That means it's still not recognizing it, sorry...

That means it's still not recognizing it, sorry it took so long to respond. Had to make an emergency trip to CDC.

All boost related files are all the files within the Boost folder with all the...
Forum: RNA Sequencing 07-24-2012, 10:25 AM
Replies: 17
Views: 7,706
Posted By Aholton
LD_LIBRARY_PATH=/path/to/boost/lib:$LD_LIBRARY_PAT...

LD_LIBRARY_PATH=/path/to/boost/lib:$LD_LIBRARY_PATH

Try typing that command, the "/path/to/boost/lib" for you would be "/usr/local/lib". The only other thing I can think that I did differently...
Forum: RNA Sequencing 07-23-2012, 10:53 AM
Replies: 17
Views: 7,706
Posted By Aholton
Nevermind everyone! The export command worked, I...

Nevermind everyone! The export command worked, I was really exhausted when I tried to fix one of the servers using the export command but I was using it in the wrong server (silly me). Thank you for...
Forum: Bioinformatics 07-23-2012, 08:59 AM
Replies: 11
Views: 2,091
Posted By Aholton
Thank you for the quick explanation, I'll be...

Thank you for the quick explanation, I'll be scouring that paper during lunch today. Hopefully it can put some things into perspective for me.
Forum: RNA Sequencing 07-22-2012, 05:42 PM
Replies: 17
Views: 7,706
Posted By Aholton
Error: segment-based junction search failed with...

Error: segment-based junction search failed with err =127
/usr/local/bin/segment_juncs: error while loading shared libraries: libboost_thread.so.1.50.0: cannot open shared object file: No such file...
Forum: RNA Sequencing 07-20-2012, 11:05 AM
Replies: 17
Views: 7,706
Posted By Aholton
Thanks for the quick response, I have Tophat,...

Thanks for the quick response, I have Tophat, Boost, bowtie2, and samtools all located within my /usr/local folder, i installed them all from there and have all the libraries set to default...
Forum: RNA Sequencing 07-20-2012, 10:28 AM
Replies: 17
Views: 7,706
Posted By Aholton
Question Boost library error, running Tophat

Been fighting with Tophat installation and finally got everything setup (I think). Then I get an error about Boost (which I had the most problems with due to permissions being denied). This is the...
Forum: Bioinformatics 07-20-2012, 08:38 AM
Replies: 11
Views: 2,091
Posted By Aholton
Thanks! I tried to Google it to understand more,...

Thanks! I tried to Google it to understand more, but I was quickly lost in all the jargon that was being used.
Forum: Bioinformatics 07-19-2012, 10:51 AM
Replies: 11
Views: 2,091
Posted By Aholton
Ok so if I was to write a guide for this, what is...

Ok so if I was to write a guide for this, what is the Tophat/Bowtie part actually doing to the sequence? Is it lining them up to where they are easier to read?
Forum: Bioinformatics 07-19-2012, 10:44 AM
Replies: 11
Views: 2,091
Posted By Aholton
They are in Fastq format, I ran them through...

They are in Fastq format, I ran them through Clean_reads to cut out some of the lesser quality parts. First time doing all this so hopefully I'm on the right track.

Currently trying to get the...
Forum: Bioinformatics 07-19-2012, 10:38 AM
Replies: 11
Views: 2,091
Posted By Aholton
Thanks for the fast response, think I'll edit the...

Thanks for the fast response, think I'll edit the title and try again. Mainly just wanted to know which program would be able to compare the two sequences and tell me what was different about them.
Forum: Bioinformatics 07-19-2012, 09:05 AM
Replies: 11
Views: 2,091
Posted By Aholton
New to Bioinformatics

Hello, I am new to Bioinformatics and it's software. I was wondering if I could ask a sample question and see what discussions came up so I could learn a bit more about it.

Let's say I have 2 RNA...
Forum: Introductions 07-19-2012, 08:55 AM
Replies: 0
Views: 712
Posted By Aholton
Good afternoon/morning

My name is Ashton and I'll be working on Bioinformatics with flu viruses and the like. I'm stopping by to get ask a couple questions and get a feel for Bioinformatics since I have no background and...
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