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Forum: Academic/Non-Profit Jobs 08-16-2017, 04:12 AM
Replies: 0
Views: 758
Posted By ulz_peter
PhD opportunity in Graz/Austria on liquid biopsies for early cancer detection

My colleague Ellen Heitzer will offer a PhD position at the Medical University Graz / Austria, starting from the beginning of next year. Application deadline will be September 17. This PhD will be...
Forum: Bioinformatics 05-18-2015, 02:50 AM
Replies: 138
Views: 64,834
Posted By ulz_peter
Hi JM, Newer versions of Picard do not come...

Hi JM,

Newer versions of Picard do not come with a bunch of jar files per command, but with a unified jar file where the command you want to execute can be specified (the version I use currently...
Forum: Metagenomics 11-04-2014, 05:08 AM
Replies: 13
Views: 4,730
Posted By ulz_peter
You could give that a try: ...

You could give that a try:
https://snowman.genome.tugraz.at/snowman/
Forum: General 10-21-2014, 09:36 PM
Replies: 9
Views: 1,804
Posted By ulz_peter
Just another thought: As sequencing prices drop,...

Just another thought: As sequencing prices drop, target enrichment is a cost-factor. LIbrary preparation for WGS is easier and cheaper than for WES.
Forum: Bioinformatics 05-02-2013, 02:43 AM
Replies: 29
Views: 15,820
Posted By ulz_peter
is there any reason you spcified the -pPM...

is there any reason you spcified the -pPM parameters?

if you've got two fastq files skip the -p option. And I#m not sure about the P option; for a first shot give it a try like that:

bwa mem...
Forum: Bioinformatics 05-02-2013, 02:26 AM
Replies: 29
Views: 15,820
Posted By ulz_peter
With the -p parameter you specify the prefix. In...

With the -p parameter you specify the prefix. In the bwa mem command you need to give it the exact same prefix as you specified using the -p argument of the index step:

Hence: drop the .fa suffix...
Forum: Bioinformatics 03-12-2013, 12:29 AM
Replies: 4
Views: 1,406
Posted By ulz_peter
http://www.cytoscape.org/

http://www.cytoscape.org/
Forum: Sample Prep / Library Generation 09-18-2012, 10:27 PM
Replies: 5
Views: 4,743
Posted By ulz_peter
The high DNA concentration after PCR might also...

The high DNA concentration after PCR might also be caused by dNTPs only, since Nanodrop can't distinguish between unbound nucleotides and a PCR product.
Forum: Bioinformatics 09-13-2012, 03:27 AM
Replies: 12
Views: 1,721
Posted By ulz_peter
That's what I am guessing too, however his files...

That's what I am guessing too, however his files seem to be annotated already...
Forum: Bioinformatics 09-13-2012, 03:26 AM
Replies: 12
Views: 1,721
Posted By ulz_peter
So you've got 160 Excel files each having about...

So you've got 160 Excel files each having about 4million entries?

I guess you'll need some programming here...
I don't know of any program which could compute significance of certain SNPs when...
Forum: Bioinformatics 09-13-2012, 02:18 AM
Replies: 12
Views: 1,721
Posted By ulz_peter
what do you mean by significant SNPs? It...

what do you mean by significant SNPs?

It seems that your SNPs are already annotated.
So, in case you search for the cause of a rare disease you could limit yourself to SNPs having an allele...
Forum: Bioinformatics 09-12-2012, 10:44 PM
Replies: 12
Views: 1,721
Posted By ulz_peter
Are these SNPs annotated in any way (e.g.: Allele...

Are these SNPs annotated in any way (e.g.: Allele frequencies in 1000genomes project, Exome sequencing project, Prediction values of SIFT, Conservation Score, AminoAcid Change, gene affected)?
IF...
Forum: The Pipeline 08-03-2012, 03:53 AM
Replies: 103
Views: 139,723
Posted By ulz_peter
They actually always write MinION which looks...

They actually always write MinION which looks like an acronym (maybe the N stands for Nanopore). Just guessing though
Forum: Illumina/Solexa 08-02-2012, 02:44 AM
Replies: 11
Views: 2,305
Posted By ulz_peter
Hi guys, We were doing amplicon sequencing for...

Hi guys,
We were doing amplicon sequencing for the MiSeq. But we always spiked these samples into other runs to get the diversity needed.

Why not do the PCR with sequence-specific primer that...
Forum: Bioinformatics 06-25-2012, 11:29 PM
Replies: 1
Views: 922
Posted By ulz_peter
The lonesome "M" in the middle of the text is...

The lonesome "M" in the middle of the text is IUPAC Ambiguity Code. This is used if you want to state that two or more bases are likely to be in the same position. In this case the letter M is short...
Forum: Bioinformatics 06-17-2012, 09:58 PM
Replies: 4
Views: 4,292
Posted By ulz_peter
Our MiSeq FastQs are output using Sanger encoding...

Our MiSeq FastQs are output using Sanger encoding (33 offset to the phred score), which should be the same as Illumina1.8+.
Forum: General 04-17-2012, 09:17 PM
Replies: 1
Views: 1,290
Posted By ulz_peter
have you tried searching the sra? ...

have you tried searching the sra?
http://www.ncbi.nlm.nih.gov/sra/

you could try searching for whole-genome sequencing of humans like this:
human[organism] whole-genome
Forum: Bioinformatics 04-13-2012, 12:44 AM
Replies: 138
Views: 64,834
Posted By ulz_peter
in case the barcodes are still in your sequence...

in case the barcodes are still in your sequence you need to trim them out, they could cause serious trouble in downstream analyses. However, for our MiSeq we get the index reads as separate fastq...
Forum: Bioinformatics 04-12-2012, 11:09 PM
Replies: 138
Views: 64,834
Posted By ulz_peter
That's a good question. Those files correspnd to...

That's a good question. Those files correspnd to contigs that have not been reliably placed on a chromosome due to problematic sequences. I personally just use chr1-22 X, Y and M. There should be...
Forum: Bioinformatics 04-12-2012, 10:03 PM
Replies: 138
Views: 64,834
Posted By ulz_peter
thanks a lot. Up to now, there was no need to...

thanks a lot. Up to now, there was no need to remove adaptor sequences from the exome-sequencing data we got. However, for other experiments I was using the cutadapt tool...
Forum: Bioinformatics 04-11-2012, 09:38 PM
Replies: 5
Views: 4,977
Posted By ulz_peter
You could better differentiate between Exome and...

You could better differentiate between Exome and RNA-seq reads by watching the mean insert size, since aligning RNA-seq reads that span exons would lead to long insert sizes and/or split-reads. If...
Forum: Bioinformatics 04-10-2012, 03:41 AM
Replies: 15
Views: 6,028
Posted By ulz_peter
I was able to reproduce your error: I just put in...

I was able to reproduce your error: I just put in a wrong prefix index and wrong sai files. It seems bwa uses sam bam_reader functions to read the native .sai format (that's why the error appears...
Forum: Bioinformatics 03-01-2012, 12:15 AM
Replies: 6
Views: 2,342
Posted By ulz_peter
Cram

Hi Guys,

Anyone already thought about deploying CRAM for archiving alignment data, rather than BAM?

http://www.ebi.ac.uk/ena/about/cram_toolkit

Our Illumina representative told us they want...
Forum: Bioinformatics 02-15-2012, 04:18 AM
Replies: 4
Views: 2,682
Posted By ulz_peter
a very popular algorithm for 454 reads is SSAHA2

a very popular algorithm for 454 reads is SSAHA2
Forum: Bioinformatics 02-09-2012, 10:48 PM
Replies: 2
Views: 1,479
Posted By ulz_peter
Hi vinila, By typing make you just compile the...

Hi vinila,
By typing make you just compile the program, you do not actually install it. Instead the code in which it was written is translated in computer language. Some programs do offer a make...
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