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Forum: Illumina/Solexa 02-18-2015, 05:54 PM
Replies: 3
Views: 2,118
Posted By dlawrence
HiSeq2500 - how to sequence pair after single end run

Our machine was prepped for a Paired End run, but we forgot to enter the read length for the paired read, so the machine ran it through as single end.

The job has completed, and the flow cell is...
Forum: Bioinformatics 01-28-2015, 06:14 PM
Replies: 0
Views: 1,421
Posted By dlawrence
BioGraphServ: Bioinformatics Graph Server

Hi, I would like to introduce BioGraphServ (http://biographserv.com), which is a webapp for quickly and easily generating graphs and analysis.

http://biographserv.com/

Drag & drop small...
Forum: Introductions 06-29-2014, 05:59 AM
Replies: 5
Views: 3,832
Posted By dlawrence
The % is low but not out of the ordinary. The...

The % is low but not out of the ordinary. The relative proportions of different small RNA classes can change drastically between experiments. As peterawe says, usually it is rRNA and tRNA but I have...
Forum: Bioinformatics 08-15-2013, 02:31 AM
Replies: 3
Views: 1,252
Posted By dlawrence
Tophat Paired Ends and trimming - A warning

Only 0.5% of my reads were correctly paired with Tophat. And a huge amount were mapping to a different chromosome.

I discovered the problem only occurred when I trimmed the reads first. (?)

I...
Forum: Bioinformatics 07-29-2013, 03:02 AM
Replies: 4
Views: 1,975
Posted By dlawrence
Install bedtools and then a small script like the...

Install bedtools and then a small script like the below should do it:


BAM=foo.bam
MIN_DEPTH=10

genomeCoverageBed -ibam ${BAM} -bg | awk -v "min_depth=${MIN_DEPTH}" '{split($0, cols,"\t"); if...
Forum: Illumina/Solexa 07-10-2013, 12:06 AM
Replies: 5
Views: 2,847
Posted By dlawrence
Yeah, but it would be good to die immediately...

Yeah, but it would be good to die immediately with a nice message, not cryptically 15 CPU hours later :(
Forum: Illumina/Solexa 07-09-2013, 11:27 PM
Replies: 5
Views: 2,847
Posted By dlawrence
I just had the same problem. Short answer:...

I just had the same problem.

Short answer: don't put spaces in the SampleSheet.csv fields.

Long answer:

Casava runs in multiple threads causing any errors to be interleaved with debug...
Forum: Bioinformatics 03-27-2013, 01:29 AM
Replies: 10
Views: 7,050
Posted By dlawrence
Cuffdiff p-value distributions and replicates

Hi, has anyone looked at the distribution of Cuffdiff's p-values?

As I understand it, p-values should be evenly distributed (ie flat histogram) for the null hypothesis, which should be the case...
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