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Search: Posts Made By: serenaliao
Forum: Bioinformatics 08-21-2014, 01:36 PM
Replies: 1
Views: 2,852
Posted By serenaliao
How to extract uniquely mapped paired end reads from bam file

Dear all,

I believe this questions has been partially brought up several times. But I cannot find a definite answer from all the previous discussion.

I am now working on bam files of...
Forum: RNA Sequencing 08-20-2014, 11:42 AM
Replies: 0
Views: 2,261
Posted By serenaliao
How to extract uniquely mapped paired end reads from bam file

Dear all,

I believe this questions has been partially brought up several times. But I cannot find a definite answer from all the previous discussion.

I am now working on bam files of...
Forum: Epigenetics 05-06-2014, 10:02 AM
Replies: 2
Views: 3,174
Posted By serenaliao
Hi Simon, Thanks for the reply. First...

Hi Simon,

Thanks for the reply.

First some comments to your suggestions:
1. fixed CpG windows sounds OK. But it still sounds a little arbitrary. I am wondering if there are ways to determine...
Forum: Epigenetics 05-05-2014, 02:14 PM
Replies: 2
Views: 3,174
Posted By serenaliao
Problem of methylKit: Too many false positive?

Dear all,

I have been implementing methylKit for a while for one of my project. But I feel there is a severe issue of methylKit in generating a lot of false positive.

If I understand...
Forum: Bioinformatics 08-14-2013, 11:11 AM
Replies: 0
Views: 1,706
Posted By serenaliao
Using Picard "CalculateHsMetrics" to find coverage stat

Hi all,

I have been trying to use CalculateHsMetrics to get coverage information. I have two questions:

1. When I run the code:
java -Xmx10g -jar...
Forum: Epigenetics 05-21-2013, 10:42 AM
Replies: 5
Views: 3,450
Posted By serenaliao
Just to follow up, I used awk...

Just to follow up, I used awk '{if($3!~/^chr/){$3="chr"$3} print($0)}' filename. Does this sound reasonable?
Forum: Epigenetics 05-21-2013, 10:18 AM
Replies: 5
Views: 3,450
Posted By serenaliao
Thanks fkrueger, You are right. This...

Thanks fkrueger,

You are right. This happened to my FASTA file.(some are chr<number> and some are <number>) Is there any convenient way to add "chr" before the chromosome number in SAM file(third...
Forum: Epigenetics 05-20-2013, 12:59 PM
Replies: 5
Views: 3,450
Posted By serenaliao
Wierd SAM format chromosome column

Dear all,

According to my previous experience, in sam file output by bismark, the third column is usually chromosome number with "chr" in front. While my new data has a mixture of chr<number> and...
Forum: Epigenetics 05-02-2013, 02:34 PM
Replies: 6
Views: 4,607
Posted By serenaliao
How to build reference genome for targeted region(from a BED file) for alignment?

I am working with Sureselect methylseq data. Previously we used the whole reference genome for Bismark alignment with mapping efficiency 50%~60%.
Considering most of reads should be around targeted...
Forum: Epigenetics 03-19-2013, 11:12 AM
Replies: 0
Views: 2,066
Posted By serenaliao
Annotate a bed file from Sureselect Kit(Methylseq)

Hi all,

I am working with a agilent's sureselect methylseq data. I was provided with the bed file with targeting regions but no annotations (Promoter/CpG islands/regulatory regions/DMRs/etc...) I...
Forum: Epigenetics 02-26-2013, 09:54 PM
Replies: 4
Views: 1,929
Posted By serenaliao
Hi andrew, I downloaded two samples BS from...

Hi andrew,

I downloaded two samples BS from EBI SRA. Basically, we are more interesting in Hiseq2000. I am wondering if you can answer my question. After I download sample DRR001680, I found the...
Forum: Epigenetics 02-25-2013, 07:20 AM
Replies: 4
Views: 1,929
Posted By serenaliao
Thanks, I will try those.

Thanks, I will try those.
Forum: Epigenetics 02-24-2013, 08:41 PM
Replies: 4
Views: 1,929
Posted By serenaliao
Public Mouse Methyl-seq Data?

Hi everyone,

I am looking for a public whole genome methyl-seq data, GA or hiseq to do comparison to another platform. I have actually looked into one data deposit to GEO, but it turns out their...
Forum: Epigenetics 02-21-2013, 07:11 PM
Replies: 3
Views: 2,521
Posted By serenaliao
A following question is If I use bismark...

A following question is If I use bismark methylation call extractor for the overlapped pair end reads(count the overlapped CpG twice), will the same reads actually report two CpG calling in the same...
Forum: Epigenetics 02-21-2013, 08:29 AM
Replies: 3
Views: 2,521
Posted By serenaliao
Insert size for overlapped reads?

When using bismark, if we set -I(min insert size) as 20, will sam file exclude overlapped reads? In my case 70% of pe reads in sam file are overlapped, though I set -I 20.

Is this normal?
Forum: Epigenetics 02-14-2013, 12:36 PM
Replies: 2
Views: 2,574
Posted By serenaliao
I need to automate the process since I have...

I need to automate the process since I have ~300,000 regions. For my bed file, I only have chromosome number and start end position. Will bedtool return the gene names, CpG contents? etc..
Forum: Epigenetics 02-14-2013, 11:24 AM
Replies: 2
Views: 2,574
Posted By serenaliao
Question:Most convenient way to get annotation information for a chromosome location?

Hi all,

So now my only information is the chromosome number and region location(I have multiple targeted regions), I want to find corresponding gene id/symbol(may be multiple), their Relation to...
Forum: Epigenetics 02-12-2013, 11:31 AM
Replies: 3
Views: 1,772
Posted By serenaliao
Ok, so in that case, the sequence between the two...

Ok, so in that case, the sequence between the two start position should still be mapped back to the sequence in the sam file right?
Forum: Epigenetics 02-12-2013, 09:54 AM
Replies: 3
Views: 1,772
Posted By serenaliao
Question about sam output of Bismark

I am wondering if anyone has ever encountered similar problem. I used the latest version of Bismark for my data(pair end 100bp). After a closer look at the output sam file, I found there are some...
Forum: Epigenetics 02-01-2013, 02:35 PM
Replies: 5
Views: 4,713
Posted By serenaliao
Thank you Pete. The information is really useful.

Thank you Pete. The information is really useful.
Forum: Epigenetics 02-01-2013, 07:10 AM
Replies: 5
Views: 4,713
Posted By serenaliao
Thanks dpryan. I will look into those. If you are...

Thanks dpryan. I will look into those. If you are interested we can discuss this further.
Forum: Epigenetics 01-31-2013, 05:06 PM
Replies: 5
Views: 4,713
Posted By serenaliao
Method to detect DMR

Is there any popular method to detect DMR(differential methylated regions) using Bisulfite sequencing data? I searched but didn't find many method except for some really naive ones. It seems there...
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