Steven asked that I re-run some Olympia oyster transposable elements analysis using RepeatMasker and a newer version of our Olympia oyster genome assembly.
Installed the software on both of the Apple Xserves (Emu and Roadrunner) running Ubuntu 16.04.
Followed the instructions outlined here:
Starting with the prerequisites:
1. Download and install RMBlast
- NCBI Blast 2.6.0 source - isb 2.6.0 patch
make command continually failed:
cd /home/shared/ncbi-blast-2.6.0+-src/c++ make
While trying to troubleshoot this issue, continued with the other prerequisites:
2. Downloaded Tandem Repeat Finder v.4.09
- Saved file (```trf409.linux64```) to ```/home/shared/bin```. NOTE: ```/home/shared/bin``` is part of the system PATH. See the ```/etc/environment``` file. - Changed permissions to be executable: <pre><code>sudo chmod 775 trf409.linux64</code></pre>
3. Downloaded RepBase RepeatMasker Edition 20170127 (NOTE: This requires registration in order to obtain a username/password to download the file).
4. Downloaded RepeatMasker 4.0.7
- Saved to ```/home/shared/RepeatMasker-4.0.7```
5. Installed RepBase RepeatMasker Edition 20170127 in
Currently re-building RMBlast and it takes forever… Will report back when I have it running.
from Sam’s Notebook https://ift.tt/2IFRP79
A new enchilada
(P.S. I think I really want enchiladas now)
After fixing the
bismark_methylation_extractor issue, Steven suggested I duplicate my notebook and rerun the analysis on a subset of the data. I created this notebook and started rerunning
bismark to align the sequences to the prepared genome. I then deduplicated, sorted, and indexed the .bam files, and extracted methylation calls successfully! I also completed the HTML and Summary Report steps. All outputs from this notebook can be found in this folder.
The next step is to duplicate the notebook I created today, remove the -u argument, and run the commands on the full dataset. I created this notebook and started to run the alignment. I’ll check on it in a few days!
from the responsible grad student https://ift.tt/2LoahTC
Earlier this week, I ran TrimGalore!, but set the trimming, incorrectly – due to a copy/paste mistake, as
--non-directional, so I re-ran with the correct settings.
Steven requested that I trim the Geoduck RRBS libraries that we have, in preparation to run them through Bismark.
These libraries were originally created by Hollie Putnam using the TruSeq DNA Methylation Kit (Illumina):
All analysis is documented in a Jupyter Notebook; see link below.
Overview of process:
- Run TrimGalore! with
- Run FastQC and MultiQC on trimmed files.
- Copy all data to owl (see Results below for link).
- Confirm data integrity via MD5 checksums.