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Forum: Epigenetics 05-03-2017, 08:21 AM
Replies: 6
Views: 6,033
Posted By asurarocks
Here you go: ...

Here you go:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147514
Forum: Bioinformatics 03-16-2013, 11:53 AM
Replies: 3
Views: 1,821
Posted By asurarocks
Here is what I came up with: Convert BAM/SAM...

Here is what I came up with:
Convert BAM/SAM to BED (narrowpeak), find peaks using SPP/MACS, set a cutoff for noisy peaks and obtain their intervals, use BEDTools to subtract those intervals from...
Forum: Bioinformatics 03-15-2013, 02:03 PM
Replies: 3
Views: 1,821
Posted By asurarocks
Hi metheuse, Did you figure it out? I am...

Hi metheuse,
Did you figure it out? I am dealing with a noisy medip-seq data and I wish to remove the reads that are contributing to noisy peaks. Any help will be much appreciated!
Thanks,
Forum: Epigenetics 03-15-2013, 08:12 AM
Replies: 6
Views: 6,033
Posted By asurarocks
If you are using MEDIPS package, INPUT sample is...

If you are using MEDIPS package, INPUT sample is optional. I got decent numbers of DMRs without using input sample.
Forum: Epigenetics 11-15-2012, 06:26 PM
Replies: 27
Views: 10,488
Posted By asurarocks
Input file is non-enriched seq experiment, serves...

Input file is non-enriched seq experiment, serves as a background to measure relative increase or decrease in methylation. It is totally optional. You can just go ahead with your control and...
Forum: Epigenetics 11-04-2012, 08:24 PM
Replies: 27
Views: 10,488
Posted By asurarocks
Hi fczqz, Sorry, I am not sure about those...

Hi fczqz, Sorry, I am not sure about those things. Batman takes unusually long time writing/reading database, it became unfeasible for us to use it for any of our analysis. So I don't have much...
Forum: Bioinformatics 10-31-2012, 09:07 AM
Replies: 5
Views: 1,887
Posted By asurarocks
Thanks Aaron, The review was very helpful!!

Thanks Aaron, The review was very helpful!!
Forum: Epigenetics 10-25-2012, 10:09 AM
Replies: 27
Views: 10,488
Posted By asurarocks
Hi fczqx, I think the format is correct. I no...

Hi fczqx, I think the format is correct. I no longer use batman since I switched to MeDIPS (and then to MeDUSA) for my analysis.
Forum: Epigenetics 10-24-2012, 06:08 AM
Replies: 27
Views: 10,488
Posted By asurarocks
Hi fczqx, for LoadRatsGFF I used the...

Hi fczqx,

for LoadRatsGFF I used the following syntax

java batman.LoadRatsGFFApplication -expt EXPT -dbURL jdbc:mysql://domain.edu/dbname -dbUser username -dbPass password FILE-chr2.pad.gff
...
Forum: Epigenetics 10-16-2012, 06:01 AM
Replies: 27
Views: 10,488
Posted By asurarocks
Also, If you are looking for analyzing MeDIP-seq...

Also, If you are looking for analyzing MeDIP-seq data that has replicates then you should probably try MeDUSA. A pipeline that uses MEDIPS, USeq and DESeq for finding and annotating DMRs.
Forum: Epigenetics 10-16-2012, 05:58 AM
Replies: 27
Views: 10,488
Posted By asurarocks
I see a lot of people still looking for the...

I see a lot of people still looking for the protocol for using Batman. I contacted the author and he replied me with the protocol for using Batman on MeDIP-seq. I will just paste it here:
"Here's...
Forum: Epigenetics 08-31-2012, 05:24 PM
Replies: 27
Views: 10,488
Posted By asurarocks
Luqie: Please, help us!

Luqie: Please, help us!
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