User: Newvin

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Newvin340
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7 years, 10 months ago
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8 years, 8 months ago
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b*****@umich.edu

Posts by Newvin

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Bwa Alignment Length
... These are Illumina short reads. The variation in read length occurs because we used an adaptive algorithm to trim the reads based on quality score prior to assembly. ...
written 7.8 years ago by Newvin340
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Bwa Alignment Length
... After performing a transcriptome assembly, I am using BWA to align the reads to my assembled contigs. From the resulting SAM file, I am able to calculate the # of reads that map to each contig, but I would like to normalize this abundance measure by using the length of each alignment. My naive que ...
alignment bwa written 7.8 years ago by Newvin340 • updated 3.5 years ago by Biostar ♦♦ 20
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Reads Per Contig From Sam File?
... After recently assembling a transcriptome, I took the reads used to generate the assembly and aligned them to the assembled contigs using BWA. The output of this process is a SAM file. I'd like to parse this SAM file to get a list of the # of reads map to each assembled contig. Before rolling my ...
read alignment contigs sam parsing written 7.9 years ago by Newvin340 • updated 7.9 years ago by Ahill1.6k
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Answer: A: Computational Biology Career Prospects
... I was in your position a few years back--straight CS background and 5+ years of software development experience. Before applying to bioinformatics Master's programs, I took night classes in biology (molecular & cellular, organismic & evolutionary). This was incredibly useful in both confir ...
written 7.9 years ago by Newvin340
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Comment: C: Extract Sequences From Fasta Using Awk One-Liner
... Thanks. I must have missed that in that documentation. How AWK-ward. ...
written 7.9 years ago by Newvin340
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Extract Sequences From Fasta Using Awk One-Liner
... Hi all. Really basic question here. I'd like to grab the sequences from a FASTA file with an AWK one-liner. To grab the headers, I can do: awk < seq.fasta '/^>/ { print $0 }' How do I negate this, so that it grabs the lines that do NOT begin with the '>' character. Feel free to chim ...
fasta parsing sequence awk written 7.9 years ago by Newvin340 • updated 7.9 years ago by Aaronquinlan11k
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Answer: A: Basic Bioinformatics Analysis For Cdna
... Is this raw RNA-seq data? If so, a good first step would be to QC it. FastQC works well for this purpose. Regardless, you probably want to perform some BLASTs to see what is being expressed (and by what organism if you were not given this information). You can also look at some basic statistics s ...
written 8.0 years ago by Newvin340
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De Novo Metatranscriptomic Assembly Failing - Trinity, Velvet/Oases
... I'm attempting de-novo assembly of metatranscriptomic data, which is admittedly a very resource-intensive problem. I have ~206 million paired-end Illumina reads each 100bp long generated via RNA-seq on environmental samples. I am able to create assemblies using Trinity and Velvet/Oases using a sma ...
assembly transcriptome velvet trinity written 8.0 years ago by Newvin340 • updated 5.9 years ago by Dgg3260
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Velvet "Strand_Specific" Argument
... The Velvet manual documents a "strand_specific" argument for transcriptome assembly. If this option is specified, how does the assembler ascertain the strand that a read comes from? My guess would be it looks for a trailing "/1" or "/2". Can anyone confirm this or give me a better answer. Here i ...
assembly velvet strand transcriptome written 8.0 years ago by Newvin340 • updated 6.0 years ago by SES8.2k
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Illumina Read Names: /2 Vs. /3
... The sequencing core at my university performed paired end RNA-seq on some of our lab's samples using Illumina sequencing technology. My understanding is that generally the forward and reverse read names are designated with trailing /1 and /2 e.g. D5KHLFN1_0181:1:1101:1209:2028#0/1 D5KHLFN1_0181:1 ...
read illumina paired next-gen sequencing written 8.0 years ago by Newvin340 • updated 8.0 years ago by User 124420

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