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Forum: Bioinformatics 12-07-2017, 07:36 AM
Replies: 0
Views: 433
Posted By pig_raffles
BiSeq - How to handle covariates?

Hi,

I am attempting to use BiSeq (Hebestreit et al. 2013) to delineate DMRs among treatment groups in Bismark aligned RRBS data

I have made a successful preliminary run through of the BiSeq...
Forum: Bioinformatics 10-24-2017, 10:39 AM
Replies: 649
Views: 151,404
Posted By pig_raffles
Hi Felix, I managed to get the script to...

Hi Felix,

I managed to get the script to work by having all the files (input, output) in the same directory as the bismark2Bedgraph script.

I could not find anything wrong with the file...
Forum: Bioinformatics 10-20-2017, 06:54 AM
Replies: 649
Views: 151,404
Posted By pig_raffles
Hi, I am having trouble getting the...

Hi,

I am having trouble getting the bismark2bedGraph software in the Bismark package to run. I have successfully aligned my RRBS reads to my reference genome and then used...
Forum: Bioinformatics 04-25-2017, 01:46 AM
Replies: 649
Views: 151,404
Posted By pig_raffles
Excellent, thank you for the very clear...

Excellent, thank you for the very clear explanation
Forum: Bioinformatics 04-24-2017, 06:39 AM
Replies: 649
Views: 151,404
Posted By pig_raffles
Hi, I have been using Bismark to align RRBS...

Hi,

I have been using Bismark to align RRBS read data to a reference genome. Up until now I have been using the default alignment settings with Bowtie2. However I want to find out if these are...
Forum: Bioinformatics 04-17-2017, 01:17 PM
Replies: 132
Views: 35,047
Posted By pig_raffles
Choosing minimum RRBS read length in Trim Galore!

I am new to the bioinformatic analysis of RRBS data. I am using Trim Galore! to QC and adapter trim my RRBS read data. I have generated single-end 75bp reads on an Illumina NextSeq.

The default...
Forum: Sample Prep / Library Generation 07-08-2016, 02:27 AM
Replies: 6
Views: 4,777
Posted By pig_raffles
Thanks again for the advice. This will be really...

Thanks again for the advice. This will be really useful for me and, I am sure, other people
Forum: Sample Prep / Library Generation 06-20-2016, 12:43 AM
Replies: 6
Views: 4,777
Posted By pig_raffles
Thanks for the reply, It seems like you have...

Thanks for the reply,

It seems like you have a lot of experience carrying out DNA extractions from RNAlater, have you had a chance to compare the extractions for yield/quality to those of the same...
Forum: Sample Prep / Library Generation 06-14-2016, 05:27 AM
Replies: 6
Views: 4,777
Posted By pig_raffles
Apologies for the lack of detail. I am using...

Apologies for the lack of detail.

I am using fish liver tissue.

It is a tissue that I have never had too much problem carrying out extractions with before (for ethanol stored tissue). In fact...
Forum: Sample Prep / Library Generation 06-14-2016, 02:49 AM
Replies: 6
Views: 4,777
Posted By pig_raffles
Advice on DNA Extraction from RNAlater stored tissue

Hi,

I am attempting to extract DNA from RNAlater stored tissue samples for
downstream DNA methylation sequencing (RRBS).

I have tried several different extraction protocols: Qiagen DNeasy...
Forum: Bioinformatics 07-16-2015, 07:14 AM
Replies: 0
Views: 478
Posted By pig_raffles
Extracting and classifying bacterial contamination from eukaryotic transcripts

Hi,

Not sure if this fits exactly into this forum, but here goes...

We have used Illumina sequencing to sequence the retina from a species of fish.

One aim of this study is to see whether...
Forum: RNA Sequencing 10-16-2012, 04:52 AM
Replies: 7
Views: 3,572
Posted By pig_raffles
So this was purely total RNA dissolved in...

So this was purely total RNA dissolved in RNase-free water at room temperature?
Forum: RNA Sequencing 10-15-2012, 06:35 AM
Replies: 7
Views: 3,572
Posted By pig_raffles
Hi Phillip, Thanks for replying, could you...

Hi Phillip,

Thanks for replying, could you tell me which RNase inhibitor you use and do you elute your samples in RNase-free water?
Forum: RNA Sequencing 10-11-2012, 01:03 AM
Replies: 7
Views: 3,572
Posted By pig_raffles
Total RNA stability following extraction/isolation

Hi all,

I will be extracting total RNA from animal tissue using the RNeasy minikit. The final step of which is to elute in to RNase-free water.

The next step, following extraction/isolation,...
Forum: RNA Sequencing 06-08-2012, 07:17 AM
Replies: 31
Views: 26,157
Posted By pig_raffles
DNase treatment and fragmentation of RNA

Hi all,

I have recently started RNA extraction on different fish tissues with the aim of carrying out RNA-seq using Illumina Hi-seq.

Following a Trizol extraction protocol, I performed DNase...
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