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Forum: Clinical Sequencing 04-18-2016, 12:30 AM
Replies: 4
Views: 5,355
Posted By pettervikman
For the human genome I use 1/100 in the...

For the human genome I use 1/100 in the non-coding regions and 1/1000 in the coding regions. Per individual of course. This tends to be roughly true. But it will differ between non coding regions and...
Forum: Bioinformatics 11-14-2013, 03:49 AM
Replies: 0
Views: 760
Posted By pettervikman
Combinatorial exom seq data

Hi

I'd like input with regards to how a mixture of data would behave for exom seq samples.

So, the set up is this. Straight forward, 2*101 bp HiSeq2000 runs on whole exom seq Illumina truseq...
Forum: Bioinformatics 03-28-2013, 12:11 AM
Replies: 13
Views: 5,929
Posted By pettervikman
Firstly, I thought that the coverage search...

Firstly, I thought that the coverage search defined new exons as based on coverage piles and that it then tried to map reads to the exons and junctions between all such piles. Hence reads that...
Forum: Bioinformatics 03-27-2013, 11:24 PM
Replies: 13
Views: 5,929
Posted By pettervikman
I'm afraid I don't understand your point. All...

I'm afraid I don't understand your point. All junctions/transcripts with a low number of reads are going to be hard to reconstruct. My thought is that by using coverage_search you'll get more reads...
Forum: Bioinformatics 02-21-2013, 02:57 AM
Replies: 13
Views: 5,929
Posted By pettervikman
I see the point in leaving --coverage-search off,...

I see the point in leaving --coverage-search off, especially since the samples I'm running at the moment have been stuck at this point for >3 days (2*101bp, ~40-50 million reads). I don't agree with...
Forum: RNA Sequencing 02-18-2013, 12:29 AM
Replies: 9
Views: 4,787
Posted By pettervikman
Any more info regarding this? I just realised...

Any more info regarding this? I just realised that my first 14 jobs that use --coverage-search --microexon-search have gone into junction search and they have started gobbling up memory (16-20Gb per...
Forum: Bioinformatics 02-18-2013, 12:13 AM
Replies: 13
Views: 5,929
Posted By pettervikman
But I understood the manual so that it first...

But I understood the manual so that it first looks for splice sites based on reads overlapping several places using all the different ("GT-AG", "GC-AG" and "AT-AC") splice sites and that the...
Forum: Bioinformatics 02-17-2013, 11:39 PM
Replies: 2
Views: 2,400
Posted By pettervikman
I've also noticed that tophat (v.2.0.7) is...

I've also noticed that tophat (v.2.0.7) is extremly slow when run in conjunction with bowtie2. I was going to have a look at my options ( -r 100 -m 1 -p 1 --coverage-search --microexon-search...
Forum: Bioinformatics 02-08-2013, 03:33 AM
Replies: 0
Views: 1,470
Posted By pettervikman
Creating haplotypes from vcf/NGS data

Hi

I'm trying to create haplotypes from my NGS data and my current choice of tool is haploviewer. I have however not been able to use the family structure that I have in my data set. So to sum up...
Forum: Bioinformatics 11-28-2011, 04:51 AM
Replies: 23
Views: 13,677
Posted By pettervikman
Thanks a lot for all the answers. The reason...

Thanks a lot for all the answers.

The reason I went for the poly A tail was that from a statistical stand point a certain fraction of the reads will be from the 3' end of the transcript and these...
Forum: Bioinformatics 11-18-2011, 04:45 AM
Replies: 23
Views: 13,677
Posted By pettervikman
pmiquel: I've thought about depleting them...

pmiquel: I've thought about depleting them through the same technical pipeline as is used for rRNA depletion for example. This woun't affect the actual sequencing though, I would not get more reads...
Forum: Bioinformatics 11-18-2011, 04:38 AM
Replies: 23
Views: 13,677
Posted By pettervikman
Thanks pmiquel. Didn't know that. But I've heard...

Thanks pmiquel. Didn't know that. But I've heard that it's much more common in rna-seq experiments in comparison to dna seq, hence the poly a tail story. But your saying that it's only dependent on...
Forum: Bioinformatics 11-18-2011, 04:23 AM
Replies: 23
Views: 13,677
Posted By pettervikman
Thanks! They got sequenced here on "my" hiseq. We...

Thanks! They got sequenced here on "my" hiseq. We have a hiseq here on CRC in Malmö, and where part of Lund University/LUDC (Lund University Diabets Center).

The pulldown uses a poly T tail and...
Forum: Bioinformatics 11-18-2011, 03:58 AM
Replies: 23
Views: 13,677
Posted By pettervikman
http://img408.imageshack.us/img408/6456/perbaseseq...

http://img408.imageshack.us/img408/6456/perbasesequencecontent.png

http://img685.imageshack.us/img685/8919/duplicationlevels.png

Here are per base content and duplication levels. Since we've...
Forum: Bioinformatics 11-18-2011, 01:38 AM
Replies: 23
Views: 13,677
Posted By pettervikman
A new try for the figures ...

A new try for the figures

http://img713.imageshack.us/img713/1372/persequencequality.png
http://img217.imageshack.us/img217/5808/perbasequality.png
Forum: Bioinformatics 11-18-2011, 12:50 AM
Replies: 23
Views: 13,677
Posted By pettervikman
Thanks for all the answers. I've decided to...

Thanks for all the answers. I've decided to resequence a couple of samples to a much higher depth as well as doing some data pooling to see how things look in our system. I'm assuming that the...
Forum: Bioinformatics 11-11-2011, 02:12 AM
Replies: 23
Views: 13,677
Posted By pettervikman
Question How many reads are acceptable from an RNA seq experiment

Hi

We have data from an RNA seq experiment, 48 samples v2.5 Illumina. We had roughly the recommended number of clusters and an even distribution between the samples so we've ended up with roughly...
Forum: Bioinformatics 11-11-2011, 02:07 AM
Replies: 2
Views: 2,650
Posted By pettervikman
Hi Thanks for the reply. I've realised that...

Hi

Thanks for the reply. I've realised that the output annotation is a bit unprecise, or I don't understand the labelling. Transcripts with 0 coverage and 0 in all positions except the highFPKM...
Forum: Bioinformatics 10-31-2011, 04:41 AM
Replies: 2
Views: 2,650
Posted By pettervikman
Cool Cufflinks -g option yields many 0 FPKM transcripts and annotates them interestingly

Hi

I've just started using the -g option in the newest version of cufflinks. I've found that it then creates a whole bunch of transcripts that are specified as 0 in the FPKM, as well as in high...
Forum: Bioinformatics 11-16-2010, 03:01 AM
Replies: 8
Views: 7,191
Posted By pettervikman
Thanks for the tip. I ran bowtie-inspect manually...

Thanks for the tip. I ran bowtie-inspect manually as well and managed to create the .fa file. I then proceeded to convert my qseqs to fastq using a perl script from...
Forum: Bioinformatics 11-15-2010, 05:07 AM
Replies: 8
Views: 7,191
Posted By pettervikman
Thanks for the tip. I've asked our IT department...

Thanks for the tip. I've asked our IT department to install the older versions. Is there somewhere I can get them from? Question two, are we the only ones with this issue? Because if others are able...
Forum: Bioinformatics 11-12-2010, 10:27 AM
Replies: 8
Views: 7,191
Posted By pettervikman
Bow-tie inspect returned an error

Hi all

I'm trying to run TopHat for the first time. I've checked the installation with the complementary test data set and that worked. Now with my own data set I get that message right after it...
Forum: Introductions 11-06-2009, 12:35 AM
Replies: 1
Views: 2,297
Posted By pettervikman
Finnish families from 1600

Hi

My name is Petter and I'm currently working on deep sequencing focused on, as the title says, finnish families with from a restricted region of finland with pedigrees from the 1600s. What I'm...
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