Ignoring previously committed files

https://stackoverflow.com/questions/3833561/why-doesnt-git-ignore-my-specified-file/3833675

Sam’s Notebook: Metagenomics – Geoduck Water Sample Assembly Comparisons with MetaQuast

As part of addressing this GitHub Issue on assessing taxonomic diversity in our metagenomics samples, I decided to compare the individual sample assemblies I made on 20190327 using Megahit and the assemblies that Emma made. Emma utilized NGless on her cluster in Genome Sciences with the following scripts:

  #!/bin/bash #$ -cwd #$ -S /bin/bash #$ -o ./output #$ -e ./output #$ -l mfree=3G #$ -pe serial 16 #$ -R y # Send email when job starts, ends or runs into an error #$ -m beas #$ -M emmats@uw.edu #cause a failing process to trigger a job failure to make errors easier to catch set -eo pipefail #Initialize and load modules . /etc/profile.d/modules.sh module purge module load modules{,-{init,gs/prod}} ngless/0.10.0 #Script ngless \ /net/nunn/vol1/emmats/sequencing/geo_metaG/ngl.singleLibs \ --trace \ --keep-temporary-files \ -j $NSLOTS \ -t /data/scratch/ssd 

Grace’s Notebook: Re-do MS Stats; DIA 2015 Cgseed Updates

Today I got some more input from Emma regarding the reports to export from Skyline to analyze. I exported a new MS Stats report (the built-in one from Skyline) and also made the bioreplicates in the file accurate (details in post). Additionally, I exported a new report that includes information that should help us get to the point of comparing 23C and 29C proteins, and identifying the proteins expressed in total.

New reports

New MS Stats report
New protein list

The new protein list integrates the transitions for the each peptide. However, we are still trying to figure out how to integrate the peptides for each protein (GitHub #666).

I also spoke with Yaamini, and she told me that we should only look at proteins that have 3 or more peptides (ones that have 2 or 1 should be discarded). The ones that have more than 3 peptides, the three most abundant peptides should be used.

Re-do MS Stats with new report

New MS Stats script

Products from new MS Stats:

Thoughts on new MS Stats

I haven’t delved too much into the plots, except for the Volcano Plot.

It is very different from the one I did with the earlier MS Stats report (the one I created by hand).

The one from before had the bioreplicates wrong. I had:
| Temp trtmnt | sample day | sample | bioreplicate | |————-|————|——–|————–| | 23C | 9/11/15 | 1 | 1 | | 29C | 9/11/15 | 2 | 2 | | 23C | 9/14/15 | 13 | 1 | | 29C | 9/14/15 | 14 | 2 |

And it showed that there was 1 significantly downregulated (old volcano plot)

Today, Steven said that bioreplicates should actually be within treatment. So I fixed the bioreplicates for today’s MS Stats report and MS Stats analysis in R. The bioreplicates are now:
| Temp trtmnt | sample day | sample | bioreplicate | |————-|————|——–|————–| | 23C | 9/11/15 | 1 | 1 | | 29C | 9/11/15 | 2 | 1 | | 23C | 9/14/15 | 13 | 2 | | 29C | 9/14/15 | 14 | 2 |

Maybe that’s why the new Volcano plot has no significant proteins and the last plot did.

Next steps:

I also spoke with Yaamini, and she told me that we should only look at proteins that have 3 or more peptides (ones that have 2 or 1 should be discarded). The ones that have more than 3 peptides, the three most abundant peptides should be used.

  • Get protein lists: total proteins, and (if temp trtmnts are different) proteins for each temp trtmnt
  • Clean up repo: readme files; only include important stuff
  • Finish paper by April 17th

from Grace’s Lab Notebook https://ift.tt/2UBmzj7
via IFTTT

Yaamini’s Notebook: April 2019 Goals

IMG_0173

It’s cherry blossom season! Which also means I’m back from vacation and it’s time to set some new goals.

March Goals Recap:

Virginica:

Gigas Broodstock:

  • Putting this on hold until I can figure out how to deal with low-volume samples

Other:

April Goals

Virginica:

  • Revise methods and results for general methylation and DML descriptions
  • Modify paper repo so analysis is easily reproducible
  • Conduct gene-level analysis
  • Sort out issues with DMR and methylKit
  • Draft full paper

Virginica Sperm:

  • Identify samples for RNA-Seq
  • Extract DNA from mantle samples
  • Do MBD for sperm and mantle DNA

Other:

  • Find GSR
  • Schedule new committee meeting

// Please enable JavaScript to view the comments powered by Disqus.

from the responsible grad student https://ift.tt/2YJAm6p
via IFTTT