Friday 7/14/17:
I am having trouble running the Genome Research paper's UMI-tools. After following the INSTALL instructions from their repository I am given the following error:
[garrettp@n2010 UMI-tools]$ python setup.py install --garrettp
('Version detected:', LooseVersion ('0.6'))
Traceback (most recent call last):
File "setup.py", line 15, in <module>
"umi_tools requires setuptools 1.1 higher")
ImportError: umi_tools requires setuptools 1.1 higher
I also had trouble installing setuptools and was given a permission error. I have not been able to get around the permission error to install setuptools yet.
When I try to index the example.bam file by following their instruction
samtools index example.bam
I get an error because I don't have the samtools command.
Monday 7/17/17
Genome Research UMI-tools: Created an issue on github to resolve why I haven't been able to install setup.py
$ python setup.py install --user
returns a lengthy error ending with
IOError: Could not build the egg.
Tuesday 7/18/17
Determined that my problem is that I don't have permission to update setuptools.
Contacted HPC support for help.
Continued revising "extract reads" wiki
Wednesday 7/19/17
Troubleshot umi_tools
Thursday 7/20/17
Studied the biological terms from UMI-Reducer extract reads wiki.
installed umi_tools, but couldn't run commands.
Friday 7/21/17
Annotated Reviewer Comments on UMI-Reducer
Annotated extract reads wiki
Monday 7/24/17
Troubleshot umi_tools
Tuesday 7/25/17
Successfully ran umi_tools dedup on example.bam and logged results
Wednesday 7/26/17
Updated format of raw reads wiki.
Started researching "A survey of best practices for RNA-seq data analysis"
Thursday 7/27/17
Researched samtools rmdup and picard tools
Monday 7/31/17
Studied "A survey of best practices for RNA-seq data analysis"
Tuesday 8/1/17
Studied "How to deduplicate PCR"
Monday 8/14/17
Updated powerpoint presentation
Tuesday 8/15/17
studied collapsePCRduplicates.py to add option
Wednesday 8/16/17
studied collapsePCRduplicates.py and worked on powerpoint
Thursday 8/17/17
studied collapsePCRduplicates.py and worked on powerpoint
Friday 8/18/17
Practiced powerpoint
Sunday 8/20/17
edited collapsePCRduplicates.py to work with genome research paper example
Monday 8/21/17
ran collapsePCRduplicates.py on genome research paper example, but still needs work.
Tuesday 8/22/17
Troubleshot collapsePCRduplicates.py