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Forum: Bioinformatics 05-20-2012, 10:34 PM
Replies: 20
Views: 8,912
Posted By bpetersen
Am I the only one with this issue? I still can't...

Am I the only one with this issue? I still can't figure out what the problem is, in other datasets Varscan worked fine for me, but if this isn't fixed I'm going to have to use a different tool...
Forum: Bioinformatics 05-15-2012, 03:59 AM
Replies: 20
Views: 8,912
Posted By bpetersen
Hello everyone, I'm currently also experiencing...

Hello everyone,
I'm currently also experiencing problems with Varscan somatic, but they seem different from what has been described here. I've tried using the -B option for samtools pileup, but...
Forum: General 05-13-2012, 11:49 PM
Replies: 2
Views: 3,702
Posted By bpetersen
I would also be interested in the exact steps to...

I would also be interested in the exact steps to use for finding somatic mutations with samtools, any new insights yet?
Forum: Bioinformatics 09-07-2011, 11:24 PM
Replies: 3
Views: 3,363
Posted By bpetersen
I've also been wanting to try the above script...

I've also been wanting to try the above script for exome data, but I can't get their script for converting vcf to their ibs format to work on vcf files generated by samtools. How did you get it to...
Forum: Bioinformatics 05-18-2011, 11:18 PM
Replies: 65
Views: 15,159
Posted By bpetersen
I tried it again after removing the header of my...

I tried it again after removing the header of my samfile and the previous error is gone, but now I get the following:

=======================1=======================
>>> STEP 1: reducing files
...
Forum: Bioinformatics 05-18-2011, 01:04 AM
Replies: 65
Views: 15,159
Posted By bpetersen
Thanks for the quick reply! I am using the...

Thanks for the quick reply!
I am using the following syntax:
java NGSrich -r /path/to/file.sam -a hg18 -T /path/to/temp_folder -t /path/to/sure_select_targets.bed
The sam file was generated with...
Forum: Bioinformatics 05-18-2011, 12:15 AM
Replies: 65
Views: 15,159
Posted By bpetersen
Yes, my data are from human samples. But I get...

Yes, my data are from human samples. But I get the following error:
=======================1=======================
>>> STEP 1: reducing files

Exception in thread "main"...
Forum: Bioinformatics 05-18-2011, 12:04 AM
Replies: 65
Views: 15,159
Posted By bpetersen
Dear Peter and Ali, Your tool sounds great! I...

Dear Peter and Ali,
Your tool sounds great! I just have a question about its usage.
I get an error when trying it out, but this might be because I probably specified the wrong file for the...
Forum: Bioinformatics 03-14-2011, 11:04 PM
Replies: 5
Views: 3,589
Posted By bpetersen
Thank you so much for all your answers! I guess...

Thank you so much for all your answers! I guess given the reasons for more mismatches than specified, I will keep those alignments. It doesn't seem to affect too many reads (from what I see in IGV),...
Forum: Bioinformatics 03-14-2011, 12:25 AM
Replies: 5
Views: 3,589
Posted By bpetersen
Illumina mapping with bwa

I've been searching the forum for an answer for this, but couldn't find exactly what I was looking for. If a thread answering my question already exists, I would be grateful if someone pointed me to...
Forum: Bioinformatics 02-17-2011, 02:35 AM
Replies: 5
Views: 2,169
Posted By bpetersen
I haven't worked with using only one reference,...

I haven't worked with using only one reference, but I think you should just give it a try. I can't see why it shouldn't also work.
Forum: Bioinformatics 02-11-2011, 12:35 PM
Replies: 5
Views: 2,169
Posted By bpetersen
The cmaps we are using for bioscope consist of...

The cmaps we are using for bioscope consist of three columns:
1: number of chromosome (1-25)
2: chromosome name (chr1, chrM etc.)
3: path to fasta sequences of the single chromosomes
Hope this...
Forum: Bioinformatics 02-09-2011, 11:15 PM
Replies: 11
Views: 2,934
Posted By bpetersen
At the risk of this being a stupid question: What...

At the risk of this being a stupid question: What exactly are these "random" chromosomes? I stumbled over this when converting a soap alignment to bam. I think alignments to these random chromosome s...
Forum: Bioinformatics 11-24-2010, 07:22 AM
Replies: 16
Views: 4,883
Posted By bpetersen
I think you're looking for the term "readthrough...

I think you're looking for the term "readthrough mutation".
Have a nice day!
Forum: Bioinformatics 11-05-2010, 12:55 AM
Replies: 0
Views: 1,577
Posted By bpetersen
Freely available control exome data?

Dear all,
First of all thank you so much to everyone sharing their knowledge in this forum, it has helped me so much when starting to work in the field of bioinformatics!
Now to my question:
I've...
Forum: Bioinformatics 09-16-2010, 10:57 PM
Replies: 1
Views: 2,052
Posted By bpetersen
As far as I know, the Cambridge sequence is the...

As far as I know, the Cambridge sequence is the one now being used by the majority. It's also supposed to be implemented in hg20. We've also just switched to the Cambridge reference .
So that's what...
Forum: Bioinformatics 09-14-2010, 05:31 AM
Replies: 13
Views: 6,758
Posted By bpetersen
I am also currently trying to find out the best...

I am also currently trying to find out the best way to handle exome sequencing data (sureselect, sequenced on the solid).
It seems to me, that most people map against the whole genome, not an exome...
Forum: SOLiD 08-25-2010, 10:27 PM
Replies: 13
Views: 4,540
Posted By bpetersen
The reads you are talking about are not the SOLiD...

The reads you are talking about are not the SOLiD mate-pairs, but PAIRED-END. These are different from the mate-pairs, because library prep is the same as with fragment, but you get more data by...
Forum: Bioinformatics 07-07-2010, 10:19 PM
Replies: 5
Views: 3,299
Posted By bpetersen
I think the problem might also be different names...

I think the problem might also be different names used for your reference sequences in your reference and the sam header (or the origin of it). I've been using Bioscope and had the same problem when...
Forum: Bioinformatics 06-18-2010, 03:03 AM
Replies: 7
Views: 3,828
Posted By bpetersen
Does anyone know if PerM will support the new...

Does anyone know if PerM will support the new SOLiD paired-end sequencing data anytime soon?
In the manual it only mentions mate-pairs and I think it needs some adjusting to also handle paired-end,...
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