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Search: Posts Made By: keithforest
Forum: Bioinformatics 11-05-2013, 06:18 AM
Replies: 3
Views: 1,754
Posted By keithforest
RSEM (http://deweylab.biostat.wisc.edu/rsem/) and...

RSEM (http://deweylab.biostat.wisc.edu/rsem/) and eXpress (http://bio.math.berkeley.edu/eXpress/) are two tools that can estimate expression for unigenes without a genome reference.
Forum: Bioinformatics 11-04-2013, 06:23 AM
Replies: 8
Views: 1,895
Posted By keithforest
my approach

The analysis that convinced my lab to switch from cuffdiff to edgeR/DESeq (a few years ago, so the results may be different now with updated tools):

1. Do differential analysis using cuffdiff and...
Forum: Bioinformatics 09-24-2013, 09:22 AM
Replies: 15
Views: 9,667
Posted By keithforest
@blahah404 The gapfiller/cap3 approach does sound...

@blahah404 The gapfiller/cap3 approach does sound interesting. With that many transcriptomes, what was your method of choice in terms of data normalization/preprocessing and assembly?

@dampor...
Forum: Bioinformatics 09-21-2013, 01:57 PM
Replies: 4
Views: 2,963
Posted By keithforest
From my experience, you may be best off combining...

From my experience, you may be best off combining all reads and making a single transcriptome assembly. Then mapping reads (preferably with replicates) back to the unified assembly would allow you...
Forum: Bioinformatics 09-20-2013, 07:30 AM
Replies: 15
Views: 9,667
Posted By keithforest
I've tried assembling combined reads vs....

I've tried assembling combined reads vs. assembling separate reads for several species, and combining reads has always given a more contiguous and accurate assembly.

If you have > 200 million...
Forum: Bioinformatics 09-04-2013, 06:36 AM
Replies: 0
Views: 1,895
Posted By keithforest
SOAPdenovo-Trans and IDBA-Tran for transcriptome assembly

I was wondering if any users have experience using SOAPdenovo-Trans and/or IDBA-Tran for transcriptome assembly.

I have had reasonable results using Oases and Trinity, but I was curious if anyone...
Forum: General 02-24-2011, 03:40 PM
Replies: 1
Views: 2,937
Posted By keithforest
mouse bone marrow rna-seq data

I'm new to the forum, so my apologies if there is a better place for this question.

I am looking for rna-seq data from mouse bone marrow. Does anyone know if any is available, or where to look...
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