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RobertsLab / project-olympia.oyster-genomic

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Progress on genome #35

Open sr320 opened 6 years ago

sr320 commented 6 years ago

Lets decide how we go with this. I think it makes sense to test current assembly with real data that needs analysis to gauge status.

I sugget two ways forward - More PacBio or Nanopore....

ksil91 commented 6 years ago

Do you want me to map the 2b-RAD stuff to a new assembly to determine mapping efficiency and percentage of mapping >1?

sr320 commented 6 years ago

I am happy to do it if you can provide a couple of files to test

ksil91 commented 6 years ago

In the /web/wetgenes/2brad_201512_ca folder on owl, there are a few cleaned/filtered fastq files that you can map. The file ca_2brad_201512.out summarizes how many reads passed filtered in the final QC step. I'm working with Sam to get more files uploaded, I'm having issues with sftp currently.

sr320 commented 6 years ago

I am getting 80%+ alignment... seems good to me?

kubu4 commented 6 years ago

At some point after this, @sr320 talked about mapping the full set. I did this back in May (!!) and, apparently forgot about it!

So, here it is!

I mapped all of the 2bRAD data with had using Bowtie2. Here's notebook:

http://onsnetwork.org/kubu4/2018/05/26/read-mapping-olympia-oyster-2brad-data-with-bowtie2-on-mox/

Mapping summary:

729797535 reads; of these: