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Forum: Bioinformatics 06-12-2013, 05:57 AM
Replies: 3
Views: 1,292
Posted By chipnewb
So for example let's say we have the following: ...

So for example let's say we have the following:

5' GGGGTTTTAAAA 3' (simply for ease of illustration).
3' CCCCAAAATTTT 5'

After Illumina is done with it you will have 4 reads:

read1 = GGGG,...
Forum: Bioinformatics 06-12-2013, 05:50 AM
Replies: 3
Views: 1,292
Posted By chipnewb
Thank you. I worked out Illumina's process by...

Thank you. I worked out Illumina's process by hand last night and it turns out that for every sheared double-stranded DNA you generate, Illumina will generate a 4 reads (2 for each strand). In the...
Forum: Bioinformatics 06-11-2013, 12:46 PM
Replies: 3
Views: 1,292
Posted By chipnewb
Illumina adapters bind equally to both strands?

When looking at paired-end sequencing:

I noticed that during ChIP-seq, the adapters bind to both ends of a polished double-stranded DNA molecule. If we focus on a particular fragment of DNA,...
Forum: Bioinformatics 02-20-2013, 06:42 AM
Replies: 0
Views: 943
Posted By chipnewb
Exclamation Non-unique alignment > 95% !!!

Hi guys,

After running some quality control on my bam files (removing (a) reads not passing chastity and (b) reads not aligned) I used Partek's FLOW to analyze the resulting files. What's showing...
Forum: Bioinformatics 01-31-2013, 07:50 AM
Replies: 0
Views: 1,953
Posted By chipnewb
Question BAM file containing ALL reads, next step?

Hi guys, I'm new to this forum and new to ChIP-seq so forgive my ignorance and the broadness of my question.

I recently obtained two bam files from a company which states that the files they...
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