David John Ortiz Rivera

Short Bio:

Greetings, my name is David John Ortiz Rivera. I was born one august day in Bayamon, Puerto Rico, but raised in Morovis. Currently a 4th year undergrad student at the University of Puerto Rico, Rio Piedras. I'm primarily interested in programming, video games, music, films, and science (somewhat). In the future I like to be involved in the areas of hardware repair, cybersecurity, software engineering, videogame development, and web development.

Contact:

  • e-mail: david.ortiz11@upr.edu
  • Github: https://github.com/kytrnd

Research Goals:

  • Find if there is any gene convergence for 3 lineages of cave fishes (Stygi, Sino, Astyanax).
  • Find DGE using RNAseq from Salmon
  • Complete this semester's project

Research Description:

Phylogeny Project description:

  • Working under the supervision of Prof. Humberto Ortiz Zuazaga, Ricardo Betancourt, and Dahiana Arcila I was trying to find Diferential Expressions from different species of fishes (Astyanax, Styygicthys, Sinocheilus) through data obtained from transcriptomics to determine if there is any genetic convergence.

  • step 1 : de novo assembly on Stygicthys raw data files using Trinity.

  • step 2 : mapping our assembled files against 14,000 transcriptomes using bowtie2.
  • step 3 : obtain our sam output and convert it into quantification tables using RSEM.
  • step 4 : Visualize our DGE data to determine if there is any convergence between these species using eBseq or edgeR.
  • more on this here: https://github.com/kytrnd/Bioinformatics .
  • Quantification and Differential Expression of RNAseq with salmon (more on this soon): ++ http://2016-aug-nonmodel-rnaseq.readthedocs.io/en/latest/quantification.html.

Weekly Reports:

Second Semester (2016-2017)

Weeks 29, 30, 31, 32, 33, 34, 35, & 36 (14th of April, 2017 to 9th of June, 2017)

  • Walter's script didn't work.
  • Managed to produce the MA plots for 2D, 6D & 20D post injury VS uninjured (norm) by creating my own scripts.
  • All that is left is to analyze my results, make sure that this is all I need to write my official report.
  • Started to write my draft report, will be done in a week or two.
  • Met with Dahiana to see if we could finish our fish project, but have not heard any more from her.
  • Have not yet met with my PI, will figure that out very soon.
  • Weekly progress for the 8 weeks, I'd say about 20/100.

Weeks 25, 26, 27, & 28 (17th of March, 2017 to 14th of April, 2017)

  • Data was normalized. Size went from 80G to 26G while using k = 20.
  • Single-end assembly using Trinity, done.
  • Walter created some scripts for indexing and quantifying using Salmon , but I had to troubleshoot and correct them multiple times.
  • Managed to get the Salmon index of the assembled pepino transcriptome using k = 31.
  • Ran the quantifying script using quasi mapping, recieved a warning from Salmon saying that some percentage (can't remember) wasn't able to map, due to k size.
  • Re-ran indexing and quantifying scripts, this time with k = 21, no warnings this time.
  • Salmon ran very fast, indexing I'd say took maybe 5 minutes while quantifying 12 files one after another took 20-25 mins.
  • With the 12 count files all that is left is visualize the data.
  • Extracted the name and count columns from each 12 files, to create 12 corresponding. These can be used as input for edgeR.
  • Got stuck trying to use Titu's script, but managed to produce the MDS of the 12 files and the MA plot of 2 random groups.
  • Consulted with Prof. Ortiz and now that we have the group data, we can create the MA plots of 2D, 6D & 20D post injury VS uninjured (norm). There are other groups that I don't know how to visualize, hopefully will find out eventually.
  • Walter is currently doing the MA plot scripts.
  • Almost done.
  • Weekly progress for the 4 weeks, I'd say about 60/100.

Week 24 (10th of March, 2017 to 17th of March, 2017)

  • Re-trimmed data.
  • Hopefully normalizing by tuesday & assembling by wednesday.
  • Weekly progress rating 0/100.

Week 23 (3rd of March, 2017 to 10th of March, 2017)

  • Still troubleshooting pipeline.
  • Normalizing script seems to be the most troublesome.
  • Weekly progress rating 0/100.

Week 22 (24th of February, 2017 to 3rd of March, 2017)

  • Gave my paper presentation.
  • Recieved pipeline, started modifying it for our data but it didn't work.
  • Troubleshooting pipeline, no luck.
  • Weekly progress rating 0/100.

Week 21 (17th of February, 2017 to 24th of February, 2017)

  • Reading Salmon paper.
  • Waiting on partner to create a pipeline for the data.
  • Weekly progress rating 0/100.

Week 20 (10th of February, 2017 to 17th of February, 2017)

  • Downloaded multiple versions of the raw data (12 files in total, around 83GB).
  • Suspicious size between the data that was in NCBI and the one downloaded on hulk.
  • Trimmed all 12 files, only reduced the total size to 80GB. Not sure if it's good or bad.
  • Waiting on lab partner for data normalizing scripts.
  • Dissecting the salmon paper as we speak.
  • Weekly progress rating 60/100.

Week 19 (3rd of February, 2017 to 10th of February, 2017)

  • Completed the Titus' tutorial on Salmon.
  • Started reading Salmon titled Salmon: Accurate, Versatile and Ultrafast Quantification from RNA-seq Data using Lightweight-Alignment.
  • Weekly progress rating 20/100.

Week 18 (27th of January, 2017 to 3rd of February, 2017)

  • Updated my markdown.
  • Started reading Titus' workshop on DGE using Salmon.
  • Installed Salmon
  • Weekly progress rating 20/100.

Week 17 (20th of January, 2017 to 27th of January, 2017)

  • Nothing.
  • Weekly progress rating -100/100.

Week 16 (18th of January, 2017 to 20th of January, 2017)

  • Nothing.
  • Weekly progress rating -100/100.

First Semester (2016-2017)

Week 15 (2nd of December, 2016 to 9th of December, 2016)

  • STILL have not heard from instructor on what will be my next step.
  • Nothing.
  • Weekly progress rating -100/100.

Week 14 (25th of November, 2016 to 2nd of December, 2016)

  • Have not heard from instructor on what will be my next step.
  • Nothing.
  • Weekly progress rating -100/100.

Week 13 (18th of November, 2016 to 25th of November, 2016)

  • Moved data to instructor's cluster for mapping and quantification using Bowtie-2 & RSEM.
  • Tried some scripts, no luck. Waiting on problems to be investigated.
  • Weekly progress rating 1/100.

Week 12 (11th of November, 2016 to 18th of November, 2016)

  • Changing our current mapping/quantification method (hopefully for the best).
  • Encountered problems with our mapping method for reasons unknown.
  • Weekly progress rating 0/100.

Week 11 (4th of November, 2016 to 11th of November, 2016)

  • Mapping using Bowtie-2, created only 2 files (out of 5).
  • Weekly progress rating 40/100.

Week 10 (28th of October, 2016 to 4th of November, 2016)

  • Currently re-running all my scripts to avoid corrupted data.
  • All scripts produced a Trinity.fasta file.
  • Waiting on my instructor for further work.
  • Some extra website work :(.
  • Weekly progress rating 30/100.

Week 9 (21st of October, 2016 to 28th of October, 2016)

  • Analyzed some read statistics withthe use of Transrate. Some flags popped up (low mapping percentege, size of largest contig).
  • Technical report
  • Website duty
  • Weekly progress rating 45/100.

Week 8 (14th of October, 2016 to 21st of October, 2016)

  • Started running the remaining scripts + re-ran the first 2 individuals.
  • Currently waiting on first individual assembly to finish.
  • Re-Running fastq-dump scripts.
  • Weekly progress rating 100/100 (My work here is done, everything else is frosting on the cake).

Week 7 (7th of October, 2016 to 14th of October, 2016)

  • Troubleshooting error with Individual03. Turns out that Trinity needed a large amount of RAM (256G).
  • Started running the following scripts: Individual03, Tissue01.
  • Weekly progress rating 70/100.

Week 6 (30th of September, 2016 to 7th of October, 2016)

  • Ran first Trinity script in hulk using screen commands. It was somewhat a success.
  • Started scripts for Individual02 & Individual03. Succeded only with Individual02.
  • Weekly progress rating 30/100.

Week 5 (23rd of September, 2016 to 30th of September, 2016)

  • Installed Trinity in my Makaira directory (with the help of Humberto) to avoid further problems.
  • Moved my data to HULK.
  • Weekly progress rating 20/100.

Week 4 (16th of September, 2016 to 23rd of September, 2016)

  • Makaira's Trinity kept encountering errors due to the lack of plugins.
  • Managed to download 2 Astyanax and 4 Cave/Surface fish Transcriptome files for future work.
  • Power outtage suspended all lab work after Wednesday.
  • Weekly progress rating 20/100.

Week 3 (9th of September, 2016 to 16th of September, 2016)

  • Finally met with instructor (important).
  • Took Trinity tutorial.
  • I was given data and a reference script to start assembly.
  • Created 7 scripts based on reference script and tinkering.
  • Created additional script to download cavefish and surface fish data from SRA.
  • Sadly, Trinity needs some plugins installed and SRA needs to be installed on Makaira for me to be able to use my scripts.
  • Weekly progress rating 30/100.

Week 2 (2nd of September, 2016 to 9th of September, 2016)

  • Instructor was absent this week.
  • Introduced to an Exon Capture project I'll be working on in the future.
  • Sadly no progress (again).

Week 1 (26th of August, 2016 to 2nd of September, 2016):

  • Recieved instructions to start gathering 'raw data' on different species of cave fishes.
  • Obtained data from NCBI, currently waiting on confirmation from my instructor if it's correct to proceed with assembling.
  • Sadly no progress.