Rerunning miRNA ID using merged reads

urol-e5 / deep-dive

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Rerunning miRNA ID using merged reads #40

Closed shedurkin closed 6 months ago

shedurkin commented 8 months ago

I'm going to continue rerunning the miRNA ID analyses using the merged sRNA reads while Sam is out. It looks like the current state of the analyses is:

[x] A. pulchra -- ShortStack
[x] A. pulchra -- MirDeep2
[x] A. pulchra -- BLAST
[x] P. evermanni -- ShortStack (getting errors)
[x] P. evermanni -- MirDeep2
[x] P. evermanni -- BLAST
[x] P. meandrina -- ShortStack
[x] P. meandrina -- MirDeep2
[x] P. meandrina -- BLAST

Sam, if you have any corrections/updates/tips for proceeding with these, please just let me know!

shedurkin commented 7 months ago

Realized in meeting today that most of these also need to be rerun with Jill's cnidarian mirbase database

[x] A. pulchra -- ShortStack (cnidarian miRBase)
[x] A. pulchra -- MirDeep2 (cnidarian miRBase)
[x] A. pulchra -- BLAST (cnidarian miRBase)
[x] P. evermanni -- ShortStack (getting errors) (cnidarian miRBase)
[x] P. evermanni -- MirDeep2 (cnidarian miRBase)
[x] P. evermanni -- BLAST (cnidarian miRBase)
[x] P. meandrina -- ShortStack (cnidarian miRBase)
[x] P. meandrina -- MirDeep2 (cnidarian miRBase)
[x] P. meandrina -- BLAST (cnidarian miRBase)

kubu4 commented 7 months ago

@shedurkin

So we don't end up duplicating efforts, I figured we should mention what we're working on.

I'm planning on handling the remaining P.meandrina tasks this week.

kubu4 commented 7 months ago

Actually, looks like you've taken care of P.meandrina BLAST.

It doesn't look like you've started on MirDeep2, so I'll get that going momentarily.

shedurkin commented 7 months ago

ok it looks like P.evermanni shortstack is the last thing that needs to be rerun. Any luck with debugging @kubu4? I tried it on my machine as a sanity check, and I'm getting the same error messages you noted in #39

shedurkin commented 7 months ago

I updated the manuscript results section with all of the merged reads results. @kubu4 when you get the chance could you add links to the outputs of analyses you ran?