User: lzwright

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lzwright150
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Posts by lzwright

<prev • 29 results • page 1 of 3 • next >
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Answer: A: What Is Best Strategy To Use Miseq 2X300 Reads To Improve De Novo Transcriptome
... agreed I think I will in fact try this. ...
written 4.0 years ago by lzwright150
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Comment: C: Simulation: Oases Transcriptome Assembly Infers Too Many Isoforms
... I have used Bowtie, Bowtie2, BWA and BWA-mem for mapping. I have gotten the best mapping percentages for my assembly with BWA-mem, which I believe has a higher tolerance for indels and allows gapped alignments. I then visualize the mapping on at tool like Tablet or IGV. I also calculate FPKMs to ...
written 4.0 years ago by lzwright150
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Comment: C: What Is Best Strategy To Use Miseq 2X300 Reads To Improve De Novo Transcriptome
... agreed I think I will in fact try this. ...
written 4.0 years ago by lzwright150
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Answer: A: Simulation: Oases Transcriptome Assembly Infers Too Many Isoforms
... This is a 64K question in my book -- unfortunately I don't really have an answer but it is very common for number of transcripts from de novo assembly to way exceed what is normal. For example I have done a de novo assembly of venom duct tissue and have ~200K contigs from various assemblers which i ...
written 4.0 years ago by lzwright150
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Comment: C: What Is Best Strategy To Use Miseq 2X300 Reads To Improve De Novo Transcriptome
... VO = velvet oases (sorry got lazy). are you combining new and old reads before assembling? ...
written 4.0 years ago by lzwright150
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What Is Best Strategy To Use Miseq 2X300 Reads To Improve De Novo Transcriptome Assembly Based On Hiseq 2X100 Reads?
... Hi all! First a little background: I have done a de novo transcriptome assembly of marine snail venom duct tissue using HiSeq Illumina reads. I have 289 mil PE reads of 100bp length that I have digitally normalized prior to assembly. I have used Trinity and Velvet Oases as my assemblers, and have ...
illumina hiseq miseq qualitycontrol written 4.0 years ago by lzwright150
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Comment: C: Duplicate @Sq Lines In Sam File Header
... the "source super-set" I like that :) ...
written 4.1 years ago by lzwright150
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Comment: C: Duplicate @Sq Lines In Sam File Header
... that was my first thought, something up with the contigs file. (full disclosure, I am involved in this project and had no problem running picard post BWA-mem when I was using the trinity.fasta file) These contigs are really ORFs that were generated from a subset of the Trinity contigs, using EMBOSS ...
written 4.1 years ago by lzwright150
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Comment: C: Do You Feel Good Or Bad About Putting Your Photo At Biostar?
... well I did all that but I am still blue. life goes on though. ;) ...
written 4.1 years ago by lzwright150
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Answer: A: Do You Feel Good Or Bad About Putting Your Photo At Biostar?
... I'd be willing to feel good or bad about it if I could actually upload a photo of myself and then decide. But I can't figure out how to do it.... I go to my user info, the edit tab and ..... niente. is this some kind of bioinformatics challenge? ...
written 4.1 years ago by lzwright150

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Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: The Organisation Of Really Contrived Acronyms (Orca)

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