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Search: Posts Made By: dahlo
Forum: Bioinformatics 12-16-2011, 03:05 AM
Replies: 34
Views: 18,629
Posted By dahlo
I am also amazed by this fact. Even whole genome...

I am also amazed by this fact. Even whole genome sequencing of 2-3 samples is cheap compared to having 1 person employed for a year. Still some people reason that time is something that can be wasted...
Forum: Bioinformatics 12-16-2011, 02:11 AM
Replies: 7
Views: 7,574
Posted By dahlo
Hello there I am pretty sure cufflinks can...

Hello there

I am pretty sure cufflinks can only do pairwise comparisons. If you enable the time series mode (-T/--time-series), it will only pairwise compare each time point with the next.

An...
Forum: Bioinformatics 12-16-2011, 02:07 AM
Replies: 34
Views: 18,629
Posted By dahlo
True that may be, but as NGSfan pointed out, the...

True that may be, but as NGSfan pointed out, the analysis scene is constantly changing. Say that it takes 6-12 months to make a tool user friendly. A new and better tool will come out about as often,...
Forum: Bioinformatics 12-16-2011, 01:46 AM
Replies: 5
Views: 4,133
Posted By dahlo
Bwa + gatk

Hello there

A college of mine did a lot of comparison between different combinations of aligners and SNP callers. If i remember correctly, he found that aligning the reads with BWA and using GATK...
Forum: SOLiD 10-17-2011, 06:28 AM
Replies: 12
Views: 4,215
Posted By dahlo
Oh, nice, thank you very much!

Oh, nice, thank you very much!
Forum: SOLiD 10-14-2011, 01:11 AM
Replies: 12
Views: 4,215
Posted By dahlo
Change node for licensing server?

You wouldn't happen to know if it is possible to change which computer the license server is running on? I remember we had to enter the MAC address when installing it, but we might have to change...
Forum: RNA Sequencing 09-27-2011, 07:33 AM
Replies: 4
Views: 5,478
Posted By dahlo
Does not match?

Hmm, is it just me, or does the extracted reads (with N:s in the CIGAR) not match the junctions.bed in the tophat results? When i look at the positions from junctions.bed in the BAM file with IGV...
Forum: Bioinformatics 04-15-2011, 03:24 AM
Replies: 2
Views: 3,859
Posted By dahlo
Hello Regarding the huge ratios, i think...

Hello

Regarding the huge ratios, i think they are hard to avoid. There is no other way to handle the scenarios where you have a gene that is switched on/off, that i know of.

If you were to plot...
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