Crandall - ngsQC and assemblyQC for Pseudomonas aeruginosa - FDA ARGOS BioProject

Jgergely11 commented 1 year ago

[x] Please complete ngsQC for the following organisms and all SRRs associated with each Biosample using the HIVE ngsQC protocol.
[x] Please complete assemblyQC for the following genome assembly IDs
[x] Once data is ready to be added to datasets, Check with @Jgergely11 for ngsQC and @penningtonea for assemblyQC

penningtonea commented 1 year ago

Nucleotide Refseq: NC_002516.2 Assembly Refseq: GCF_000006775.1

emdelattre commented 1 year ago

@Jgergely11 the ngsQC for May is done and ready for review. Thanks!

Jgergely11 commented 1 year ago

@emdelattre Thanks! Can you add the data to the V1.3 version of the google doc please?

emdelattre commented 1 year ago

@Jgergely11 I'm currently having issues locating the V1.3 version of the Google doc, would you be able to provide a link to the doc? So sorry about that.

Jgergely11 commented 1 year ago

@emdelattre I didn't realize you didnt have access, just added you.

emdelattre commented 1 year ago

@Jgergely11 Thank you, I just got the email. I tried opening it and was denied access, so I just requested it.

Jgergely11 commented 1 year ago

@emdelattre It looks like you should have access now, let me know if there are any issues.

emdelattre commented 1 year ago

@Jgergely11 I just checked and I still can't access the folder. I requested access again. Sorry about this.

emdelattre commented 1 year ago

@Jgergely11 I got access and put the data into the v1.3 document. Please let me know if there are any issues. Thanks again for your help!

Jgergely11 commented 1 year ago

@emdelattre thanks for adding the data. Overall it looks pretty good, but there are a few formatting issues to take care of.

Remove the empty rows between SRRs
For these organisms there is no infraspecific name so those values can be deleted
In the 'lineage' column replace all | with ; -Just find and replace within that column because there are other columns where | is needed
"schema_version" and "analysis_platform_object_id" it looks like the values were added sequentially instead of just copying down the column. The schema version should stay the same throughout the sheet (V1.3), and the object id should be consistent for each SRR
"analysis_platform" should be HIVEAWS not HIVE AWS
"sra_run_id" - remove the hyperlink
There should not be any data in "num_reads_unique" - the output from HIVE is just the total number of reads, not unique reads. Just delete all those values
There are some cells that have non-integer values from the HIVE output. Any time that happens it needs to be changed to a blank cell. I highlighted a few examples that I saw with SRR8179113.

Let me know if you have any questions

emdelattre commented 1 year ago

@Jgergely11 Thanks for the feedback, I was able to go through and fix the formatting issues. Please let me know if there is anything else that needs to be adjusted!

Jgergely11 commented 1 year ago

@emdelattre everything looks good, thank you. If I see anything else that needs your attention I'll let you know

steph-sing commented 1 year ago

work complete. closing ticket.

FDA-ARGOS / data.argosdb

Crandall - ngsQC and assemblyQC for Pseudomonas aeruginosa - FDA ARGOS BioProject #294