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Forum: Bioinformatics 10-10-2015, 03:51 AM
Replies: 4
Views: 1,246
Posted By Mocca
Having a model species gives you more...

Having a model species gives you more alternatives. Trinity genome guided worked OK for me, but its difficult to compare as I work on a non-model species. Trinity would cluster your RNAseq reads...
Forum: RNA Sequencing 10-09-2015, 10:20 AM
Replies: 1
Views: 1,107
Posted By Mocca
Check out Trinotate - took me a bit more than one...

Check out Trinotate - took me a bit more than one week to do the annotation of my de novo transcriptome (some trial and error there). The blast part (only the mandatory one) took 4 days. I also tried...
Forum: Bioinformatics 10-09-2015, 10:15 AM
Replies: 4
Views: 1,246
Posted By Mocca
Try using another assembler that handles isoform...

Try using another assembler that handles isoform resolving differently. I work with Trinity and find that good (2n vertebrate species) however it struggles a bit with paralogs and I also find...
Forum: Bioinformatics 10-09-2015, 10:04 AM
Replies: 1
Views: 888
Posted By Mocca
Have you checked out the Trinotate pipeline?...

Have you checked out the Trinotate pipeline? Quite extensive, but provides a pretty good annotation. You could run just the GO annotation steps or the whole thing using blast, signalp... I also found...
Forum: De novo discovery 10-09-2015, 09:54 AM
Replies: 2
Views: 3,245
Posted By Mocca
Discussing the quality/"completeness" of the...

Discussing the quality/"completeness" of the genome with my collaborators migth be the next step then. I also got a bit hung up on the abundance estimation analysis with the FPKM 2 cutoff where the...
Forum: De novo discovery 10-08-2015, 03:52 AM
Replies: 2
Views: 3,245
Posted By Mocca
Genome guided vs de novo - Trinity

Hi everyone,

For a while now I have been working on my de novo Trinity assembly (fish species). Using my de novo transcriptome I have been able to do some interesting differential expression...
Forum: RNA Sequencing 08-07-2013, 11:12 PM
Replies: 2
Views: 2,586
Posted By Mocca
Thanks for the reply. I didn't consider...

Thanks for the reply.

I didn't consider doing it this way. Got a bit caught up in my control samples i guess. Will give it a try!

Cheers :)
Forum: RNA Sequencing 08-07-2013, 05:32 AM
Replies: 2
Views: 2,586
Posted By Mocca
Post RNAseq time series data w/ controls for each time point

Hi everyone,

I am currently working on a RNAseq data set consisting of 4 time points where each time point has 6 challenged and 6 control individuals (not paired). I have used both DEseq and...
Forum: Introductions 03-19-2012, 11:58 PM
Replies: 373
Views: 122,142
Posted By Mocca
Hi all

I'm a PhD student working in Oslo, Norway. Just signed up here yesterday and all ready I've had lots of help from this forum. At the moment I'm working on Illumina RNAseq data. Looking forward to...
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