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Forum: Epigenetics 03-02-2015, 11:17 AM
Replies: 4
Views: 5,206
Posted By amdic2
Dear mixter, I hope you read this post even...

Dear mixter,
I hope you read this post even though you wrote about it almost 3 years ago :)
I am curently having the same problem as you did with a non-model species analyzed by RRBS.
Could you...
Forum: Epigenetics 07-24-2014, 08:05 AM
Replies: 26
Views: 10,840
Posted By amdic2
Which kit for RRBS

Dear lyndaben,
Have you decided which kit you are going to use?
I am also currently looking at several options.
The protocol published by Boyle et al. (2012) Genome Biology appears quite easy to...
Forum: Illumina/Solexa 09-01-2013, 04:54 AM
Replies: 7
Views: 8,227
Posted By amdic2
Dear ziseputi, The fragmentation used with this...

Dear ziseputi,
The fragmentation used with this kit is chemical and thus random. You can then expect your fragments <200nt to be partially lost.
Sequencing two libraries could be an option,...
Forum: RNA Sequencing 06-14-2012, 09:24 AM
Replies: 155
Views: 59,876
Posted By amdic2
Print q-value with SamWrapper

Dear all,
I am using the samWrapper function from DEGseq.
I would like to be able to get the q-values in the output of the method, as I need them in order to make a volcano plot. The problem is...
Forum: Illumina/Solexa 08-30-2011, 05:35 AM
Replies: 7
Views: 8,227
Posted By amdic2
Phillip, Thank you for the complete answer! ...

Phillip,
Thank you for the complete answer!
So it seems to me like the main difference between 4min and 8 min is the range, and not the median insert size. Am I correct?
I might try something like...
Forum: Illumina/Solexa 08-29-2011, 05:48 AM
Replies: 7
Views: 8,227
Posted By amdic2
mRNA fragmentation for 100bp paired-end reads

Hi everybody,

I am currently planning a mRNA-seq experiment in a non-model species with the first goal being to study multiple copies elements expressed in the transcriptome.

TruSeq RNA sample...
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