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Forum: Introductions 05-26-2012, 10:45 AM
Replies: 22
Views: 28,834
Posted By Heisman
Sorry, the two ends would be the reverse...

Sorry, the two ends would be the reverse complements of each other's strands.
Forum: Introductions 05-26-2012, 08:26 AM
Replies: 22
Views: 28,834
Posted By Heisman
I have never thought about this an am honestly...

I have never thought about this an am honestly not sure if you get TTT or AAA in your read.

You are correct that you sequence the ends, and if you did 2x3bp reads you would get AAA and CCC (or...
Forum: Introductions 05-09-2012, 08:38 AM
Replies: 22
Views: 28,834
Posted By Heisman
1. I don't know, as we only receive the...

1. I don't know, as we only receive the unfiltered ones. Maybe "grep -v"?

2. I think you'll need to unzip them all and then concatenate.

3. With Illumina paired end runs you have something...
Forum: Introductions 05-07-2012, 02:30 PM
Replies: 22
Views: 28,834
Posted By Heisman
Oh, right; the first reads of a fastq file for...

Oh, right; the first reads of a fastq file for Illumina will be around the edge of the flowcell, I think, making them more likely to be weird. Maybe do "less +1000000" and see what that looks like. ...
Forum: Introductions 05-07-2012, 08:29 AM
Replies: 22
Views: 28,834
Posted By Heisman
No idea if it's a problem with the library prep...

No idea if it's a problem with the library prep or the run; I would check with the sequencing core (I'd imagine it's a problem with the run, though).

There may be different numbers of files if...
Forum: Introductions 05-07-2012, 08:07 AM
Replies: 22
Views: 28,834
Posted By Heisman
1. Having stretches of N's like that is not...

1. Having stretches of N's like that is not normal. I'm not sure what the cause would be. You should check with whatever sequencing core ran those samples to see if there was anything weird with the...
Forum: Introductions 05-06-2012, 10:38 PM
Replies: 22
Views: 28,834
Posted By Heisman
No, that means (probably), that there is a 239 bp...

No, that means (probably), that there is a 239 bp DNA strand between the two adapters that were ligated on. The insert size defined like this is independent of the read length.

To explain better,...
Forum: Introductions 05-06-2012, 06:04 PM
Replies: 22
Views: 28,834
Posted By Heisman
You should read through the stickies in the...

You should read through the stickies in the Illumina library prep section. That said:

Read length and cycles are related terms. With Illumina, each base pair is sequenced one cycle at a time. So...
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