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Forum: Bioinformatics 10-28-2019, 03:45 AM
Replies: 1
Views: 638
Posted By asorbie
you can use the tximport package to import...

you can use the tximport package to import kallisto output into R and then just use DEseq2. See here:https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html
Forum: Metagenomics 09-09-2019, 04:53 AM
Replies: 4
Views: 2,454
Posted By asorbie
I think they may have changed some minor things...

I think they may have changed some minor things this year but not the entire database. 13-5 is the May 2013 release.
Forum: Metagenomics 09-09-2019, 01:31 AM
Replies: 4
Views: 2,454
Posted By asorbie
Greengenes hasn't actually been updated since...

Greengenes hasn't actually been updated since 2013. Personally, I just wouldn't use it at all. Stick to Silva, RDP or GTDB if possible.
Forum: Metagenomics 04-04-2018, 02:48 AM
Replies: 2
Views: 3,502
Posted By asorbie
From the same guys that created Metaphlan there's...

From the same guys that created Metaphlan there's also a tool called LEfSe which you could use for this. It may be easier for you if you're new to this!
Forum: General 12-04-2017, 07:31 AM
Replies: 4
Views: 1,665
Posted By asorbie
I would guess the Rhodospirillaceae are probably...

I would guess the Rhodospirillaceae are probably environmental/kit contaminants as this family is in the alphaproteobacteria class which to my knowledge is not commonly found in intestinal...
Forum: General 10-16-2017, 04:24 AM
Replies: 4
Views: 1,665
Posted By asorbie
Was this just from one mouse? Have you looked...

Was this just from one mouse? Have you looked into the possibility of other intestinal enterobacteriaceae? I work with mice/16s sequencing too and although we often find E.coli it's definitely not a...
Forum: General 08-21-2017, 05:25 AM
Replies: 2
Views: 1,452
Posted By asorbie
Can you give us a little more information, it may...

Can you give us a little more information, it may be that the unknown band is due to non-specific binding of your primers? What size is it roughly? What cycling conditions did you use, composition of...
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