User: Konrad

gravatar for Konrad
Konrad690
Reputation:
690
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Location:
Germany
Website:
http://konrad.foerstne...
Last seen:
1 year, 8 months ago
Joined:
8 years, 1 month ago
Email:
k*****@foerstner.org

Posts by Konrad

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Igb 8 Webinar Starts At 1 Pm Eastern
... Are there any recordings of this webinar available? And can I download version 8 already somewhere? The newest version on sourceforge is 7.0.4. I would really like to test it. ...
written 4.5 years ago by Konrad690
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Comment: C: Tool For Multiple Sequence Alignment Of Genomes
... Have you seen Mauve? ...
written 4.5 years ago by Konrad690
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Answer: A: Salmonella Annotation For Rna-Seq Analysis
... I assume you mean the strain SL1344 (not SL13144). If so have a look at this: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Salmonella_enterica_serovar_Typhimurium_SL1344_uid86645/ ...
written 4.5 years ago by Konrad690
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Comment: C: The Five Most Annoying Bioinformatics Problems You Face Every Week?
... Don't use excel and don't use cell colors to encode information in excel as this will get lost when you export the data to CSV files. ...
written 4.6 years ago by Konrad690
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Answer: A: Resources For Ngs?
... Maybe the NGS WikiBook is be useful for you. There is a recent publication about it. ...
written 4.6 years ago by Konrad690
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Comment: C: Have Anyone Done Bacterial Transcriptomics Using Miseq?
... I can confirm these numbers form our experiences. There are early bacterial transcriptome studies based on 454 reads with only some 100 k of reads that brought at least some helpful results. Today we aim for 3 - 5 M reads for a single bacterial transcriptome depending on the genome size and the aim ...
written 5.1 years ago by Konrad690
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Comment: C: Have Anyone Done Bacterial Transcriptomics Using Miseq?
... Maybe you can specify what you want to examine. The required depth depends on your aim. ...
written 5.1 years ago by Konrad690
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Comment: C: Questions Regarding Consensus Sequence Calling With Samtools / Bcftools / Vcfuti
... Thanks, Martjin. I was aware of the minimal (and maximal) depth parameter but not that I can use the -s parameter for the purpose of defining the ploidy. I will give it a try. ...
written 5.1 years ago by Konrad690
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Comment: C: Questions Regarding Consensus Sequence Calling With Samtools / Bcftools / Vcfuti
... Thanks, it looks like I can not pure rely on vcfutils to generate a finished sequence based on default cut-offs but have to decide some cases myself. I wanted to avoid this as this is rather subjective but good to know that this seems to be generally required. ...
written 5.1 years ago by Konrad690
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Comment: C: Questions Regarding Consensus Sequence Calling With Samtools / Bcftools / Vcfuti
... Thanks, Christof. In the end I need to have an unambiguous sequence. I personally would would interpret the S in this situation (haploid organism) as C as this is the dominating variant. But maybe there is already a common way of how to deal with this in bacterial genome re-sequencing. ...
written 5.1 years ago by Konrad690

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Student 2.9 years ago, asked a question with at least 3 up-votes. For Questions Regarding Consensus Sequence Calling With Samtools / Bcftools / Vcfutils.Pl
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