User: tptacek3050

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tptacek305060
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Posts by tptacek3050

<prev • 23 results • page 1 of 3 • next >
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Comment: C: GATK: SNP calls for variants with a single read to detect RNA editing
... What I meant by known/published is that we're not fishing for some kind of new variation, but quantifying a known/real variation. It is an addition of an A into a poly A repeat in the FAS transcript that affects function. http://www.ncbi.nlm.nih.gov/pubmed/21793106   I have VCF files (the lines i ...
written 20 months ago by tptacek305060
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GATK: SNP calls for variants with a single read to detect RNA editing
... I am working with RNAseq data to look at a known/published form of RNA editing in a certain gene. I am using GATK (and their suggested pipeline for RNAseq data) and the DepthPerAlleleBySample annotation to measure the relative quantity of the wt and edited versions of the transcripts. For some sampl ...
gatk rna-seq rna editing written 20 months ago by tptacek305060 • updated 20 months ago by geek_y8.0k
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Comment: C: Questions about using the Celera Genome Assembler for HGAP
... There was a _utgcnsfix file, but no _utgcns file. The contents of this file (1446144349_sipsey-compute-1-12.local_20669_utgcnsfix) were as follows:   CA version 8.3rc2 ($Id: utgcnsfix.C 4442 2013-10-04 14:33:50Z brianwalenz $). Error Rates: AS_OVL_ERROR_RATE 0.030000 AS_CNS_ERROR_RATE 0.100000 A ...
written 22 months ago by tptacek305060
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Questions about using the Celera Genome Assembler for HGAP
... This post is a followup to a previous post: https://www.biostars.org/p/160935/#160938   I am trying to use the PBcR pipeline for the Celera Genome Assembler (v8.3) to perform HGAP for pacbio reads (http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR).   I've got the assembler installed, and ...
celera assembler hgap pacbio written 22 months ago by tptacek305060 • updated 22 months ago by rhall160
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FASTQC and PacBio reads
... I'm working with a group that did some PacBio sequencing to aid in the assembly of some bacterial genomes.   The first priority for this group is to assess the quality of the read data. One of the formats that the read data were returned in was of fastq. We already have a pipeline for fastqc, so I ...
java memory pacbio fastqc written 23 months ago by tptacek305060 • updated 23 months ago by mjhsieh0
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Answer: A: ABySS assembly algorithm picture for presentation
... Thanks for this! ...
written 2.6 years ago by tptacek305060
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ABySS assembly algorithm picture for presentation
... I was looking for a figure for the ABySS assembly algorithm for a presentation I'm giving. I'll be presenting the de-novo assembly of a Mycoplasma species (first complete genome assembly of this species to date). ABySS was critical to the assembly of this organism's genome. I liked the figure in th ...
assembly abyss written 2.6 years ago by tptacek305060
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Answer: A: MAUVE: No gene annotations in Genbank file alignments
... Just bumping this up in case anyone knows anything. ...
written 3.1 years ago by tptacek305060
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MAUVE: No gene annotations in Genbank file alignments
... I'm trying to align 15 genbank files generated by RAST for 15 Mycoplasma genomes that we have assembled. I am aligning the files with progressivemauve with default parameters, and visualizing with MAUVE's GUI. The alignment runs fine, but when I visualize it, I get "(no annotations loaded)" for each ...
software error alignment mauve genbank rast written 3.1 years ago by tptacek305060 • updated 2.7 years ago by izwanspp10
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Comment: C: Error Running Breakdancer-Max: Max Kahan Error: 0
... The file in the example may or may not have a novel breakpoint. I have another .bam file in which there definitely should be a breakpoint detected. Now, as for IGV, the breakpoint in question is in a very difficult part of the genome (lots of repetitive sequence), so it won't be clearly visible in I ...
written 3.8 years ago by tptacek305060

Latest awards to tptacek3050

Popular Question 22 months ago, created a question with more than 1,000 views. For Error Running Breakdancer-Max: Max Kahan Error: 0
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Trouble Installing Breakdancer 1.4.2: Boost Libraries Inexplicably Not Visible

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