User: Austin Paul

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Austin Paul140
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6 years, 7 months ago
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7 years, 3 months ago
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a*******@usc.edu

Posts by Austin Paul

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Selecting Reads At Random From Fastq File
... Hi Peter, Thanks for the suggestion. For example, I have a fastq file with 50 million reads and I want to randomly select 5 million of them. It seems biopython would very easily select a single or a handful of reads with the Bio.SeqIO.index() function. Would it also be able to do the job I am in ...
written 6.6 years ago by Austin Paul140
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Selecting Reads At Random From Fastq File
... Hi, I am curious if anyone knows how to select random lines from a fastq file. There is a select random lines tool in text manipulation tools, but it does not treat fastq files specifically, so it will not group quality lines with sequence lines. And if I turn the fastq file to tabular form in ord ...
galaxy written 6.6 years ago by Austin Paul140 • updated 6.6 years ago by Jennifer Hillman Jackson25k
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Fwd: Help With Sam To Bam
... Hi Zach, You should reply to all so people dont keep working on your questions. Glad to help. Austin Date: Tue, Sep 13, 2011 at 3:10 PM Subject: Re: [galaxy-user] Help with sam to bam To: Austin Paul Thanks Austin! That did the trick. Zack You could try "fasta width formatter" on your re ...
galaxy written 6.8 years ago by Austin Paul140 • updated 6.8 years ago by Jennifer Hillman Jackson25k
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Answer: A: Help With Sam To Bam
... You could try "fasta width formatter" on your reference fasta. This has helped me in the past when I received a similar error. ...
written 6.8 years ago by Austin Paul140
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Answer: A: Extracting Reads Mapped From Bwa Mapping
... Just to emphasize the point, the difference between the two methods is an order of magnitude (for a particular example, filtering for flag type gives around 60% of reads mapping, but estimating mapped reads from pileup gave ~5% of reads mapped). Thanks, Austin ...
written 6.8 years ago by Austin Paul140
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Extracting Reads Mapped From Bwa Mapping
... Hello, I recently figured out how to filter the output bwa SAM file for flag type in order to determine the number of reads that were successfully mapped. My question is, I previously thought I could generate a pileup, then sum the number of counts for each base of the reference, and divide this n ...
alignment bwa written 6.8 years ago by Austin Paul140
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Comment: C: Line Estimation For Pileup Generation
... Hi Dannon, Thanks for telling me about that count tool. I had not used it before. So, it seems the line estimates in the history windows are a bit screwy. One pileup file I mentioned estimated ~4,000,000 lines and the count tool showed 988,000. And the other pileup file I mentioned estimated ~20 ...
written 6.8 years ago by Austin Paul140
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Line Estimation For Pileup Generation
... Hello, I am curious if the line estimation shown in the history window for pileup generation is at all accurate. I am using the pileup files to generate expression data from bwa mapping for looking at differential expression, but I am having some trouble understanding the line estimates. For exam ...
alignment bwa written 6.8 years ago by Austin Paul140 • updated 6.8 years ago by Dannon Baker3.7k
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Comment: C: Rna Seq Analysis
... Oops. Good to know. Thanks. Austin ...
written 7.1 years ago by Austin Paul140
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Comment: C: Rna Seq Analysis
... There are many ways. I typically use IGV. It needs a sam file, so I first convert the bam to sam in galaxy, then download the sam file. In IGV, I upload the reference and the sam file, then use IGVtools to index the sam file, then I can visualize the data. Austin ...
written 7.1 years ago by Austin Paul140

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