It is my first time working with RNA-Seq data, and I am having problems with Tophat and Cufflinks. Hope someone out there can give me some suggestions for the problems I encountered.
Thanks a lot,
Jie
1) Problems with tophat:
I downloaded the mouse GTF file and converted it to gff3 file ,using the script mentioned in a post from this forum, and also put the fasta file generated from the bowtie index to the folder where the bowtie indexes are.
Here are the shell script I used:
./tophat -G mouse.gff3 /path/to/indexes/ m_musculus input.fasta
And the the following output was generated:
[Wed Apr 28 18:59:09 2010] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Wed Apr 28 18:59:09 2010] Preparing output location ./tophat_out/
[Wed Apr 28 18:59:09 2010] Checking for Bowtie index files
[Wed Apr 28 18:59:09 2010] Checking for reference FASTA file
[Wed Apr 28 18:59:09 2010] Checking for Bowtie
Bowtie version: 0.12.2.0
[Wed Apr 28 18:59:09 2010] Checking reads
seed length: 37bp
format: fasta
[Wed Apr 28 18:59:15 2010] Reading known junctions from GFF file
And then the cursor went back to the system console, and the program just stopped. Although there was a folder called “tophat_out” generated, but no real output data.
Any parameters I need to adjust?
2)Problem with Cufflinks:
The system is “Ubuntu linux”.
First of all, the binary cufflinks(X86 linux version) cannot be executed. I assume it is due to the “boost” library being incorrectly installed.
Second, I tried to compile cufflinks and received error some messages when “sudo make” was executed:
Anybody has experience with the "libboost" compilation/installation? Thanks~
Thanks a lot,
Jie
1) Problems with tophat:
I downloaded the mouse GTF file and converted it to gff3 file ,using the script mentioned in a post from this forum, and also put the fasta file generated from the bowtie index to the folder where the bowtie indexes are.
Here are the shell script I used:
./tophat -G mouse.gff3 /path/to/indexes/ m_musculus input.fasta
And the the following output was generated:
[Wed Apr 28 18:59:09 2010] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Wed Apr 28 18:59:09 2010] Preparing output location ./tophat_out/
[Wed Apr 28 18:59:09 2010] Checking for Bowtie index files
[Wed Apr 28 18:59:09 2010] Checking for reference FASTA file
[Wed Apr 28 18:59:09 2010] Checking for Bowtie
Bowtie version: 0.12.2.0
[Wed Apr 28 18:59:09 2010] Checking reads
seed length: 37bp
format: fasta
[Wed Apr 28 18:59:15 2010] Reading known junctions from GFF file
And then the cursor went back to the system console, and the program just stopped. Although there was a folder called “tophat_out” generated, but no real output data.
Any parameters I need to adjust?
2)Problem with Cufflinks:
The system is “Ubuntu linux”.
First of all, the binary cufflinks(X86 linux version) cannot be executed. I assume it is due to the “boost” library being incorrectly installed.
Second, I tried to compile cufflinks and received error some messages when “sudo make” was executed:
Anybody has experience with the "libboost" compilation/installation? Thanks~
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