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Forum: Bioinformatics 12-17-2012, 09:45 AM
Replies: 2
Views: 1,258
Posted By aafc
It looks likes you've "made a huge mistake" . . ....

It looks likes you've "made a huge mistake" . . .




I think I had this exact problem when I was first trying to install cufflinks. Try this, in order:

1) Make sure LD_LIBRARY_PATH is set...
Forum: Bioinformatics 12-17-2012, 07:47 AM
Replies: 6
Views: 4,948
Posted By aafc
Yeah, COPY (in case we do something wrong) the...

Yeah, COPY (in case we do something wrong) the library files into Eigen/include. Try that. Otherwise, re-read the Eigen documentation and make sure you've installed it properly.
Forum: Bioinformatics 12-17-2012, 07:12 AM
Replies: 6
Views: 4,948
Posted By aafc
Does the Eigen directory that you installed have...

Does the Eigen directory that you installed have include as a subdirectory? Does include contain the following files and directories? :

Eigen/ <---- this is ...
Forum: Bioinformatics 12-17-2012, 07:07 AM
Replies: 5
Views: 1,765
Posted By aafc
Also, make sure $LD_LIBRARY_PATH is defined as...

Also, make sure $LD_LIBRARY_PATH is defined as the path to the dynamic boost library files (the .so files)
Forum: Bioinformatics 12-17-2012, 07:06 AM
Replies: 5
Views: 1,765
Posted By aafc
Unless the developers of cufflinks tested every...

Unless the developers of cufflinks tested every single release of boost beyond 1.47, that statement doesn't really mean much. It is possible for newer libraries to not work on software that was...
Forum: Bioinformatics 12-17-2012, 06:39 AM
Replies: 5
Views: 1,765
Posted By aafc
Try using boost version 1.47. I think I had a...

Try using boost version 1.47. I think I had a similar issue when trying using the latest version of boost, which was 1.51. The version specified by cufflinks in the manual is 1.47, I think.
Forum: Bioinformatics 12-17-2012, 06:37 AM
Replies: 6
Views: 4,948
Posted By aafc
Did you actually compile Eigen with cmake? From...

Did you actually compile Eigen with cmake? From your directory structure, it looks likes you just extracted the tarball.
Forum: Bioinformatics 12-06-2012, 08:07 AM
Replies: 1
Views: 939
Posted By aafc
I think i figured it out: Look at the...

I think i figured it out:

Look at the vingette for DESeq and see how they filtered the replicates for a specfic property in the line:

> pairedSamples = pasillaDesign$libType == "paired-end"
...
Forum: Bioinformatics 12-06-2012, 06:42 AM
Replies: 1
Views: 939
Posted By aafc
How do you specifiy specific replicates in DESeq?

I have three replicates that I made a count table for, with 6 conditions each. I am wondering how I can tell DESeq to only compare data between two replicates as opposed to accounting for all three. ...
Forum: Bioinformatics 12-04-2012, 11:24 AM
Replies: 0
Views: 1,523
Posted By aafc
Using trimmed reads with HTseq-count before DESeq?

I am doing differential expression analysis with RNA reads.

DESeq required a count table, and I am using HTSeq to make it. My paired-end illumina reads have been trimmed, and some reads have been...
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