User: Matt

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Matt110
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110
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Location:
Berkeley, CA
Website:
http://www.macmanes.com
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4 years, 6 months ago
Joined:
8 years, 9 months ago
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Posts by Matt

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Answer: A: De novo assembly for RNA-seq Illumina PE reads
... For Trinity, the only way to adjust is using the -JM setting, which you have already discovered. This only effects memory usage in 1 stage of the assembly, so not exactly sufficient. Depending on the number of reads you have, you may want to use digital normalization http://khmer.readthedocs.org/en/ ...
written 5.0 years ago by Matt110
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Comment: C: Parsing Fasta Based On Header
... how do I incorporate this into a loop.. i have several thousand records to process in this manner. ...
written 7.8 years ago by Matt110
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Parsing Fasta Based On Header
... Hi All, I have a large fasta file that I am trying to sort into multiple smaller files based on their ID's. The File starts like this: >1MUSgi|116063569|ref|NM_010065.2| AGGGG-TGGTTGACCATCAACAACATCGGCATCATG-AAGGGAGGCTCCAAGGAGTACTGGTTTGTGCTGACTGCTGAG- >2MUSgi|118130562|ref|NM_019880.3| CGGCC ...
fasta python biopython written 7.8 years ago by Matt110 • updated 7.8 years ago by John Kern60
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Cuda/Gpu Processing And Bioinformatics
... Does anybody see any progress on the horizon for leveraging GPU processing against computationally challenging problems-- e.g. de novo assembly.. I know that there are a few threads (older ones) over at seqanswers, and MUMmerGPU is one option for alignment... ...
assembly hardware written 8.8 years ago by Matt110 • updated 8.6 years ago by Alastair Kerr5.2k

Latest awards to Matt

Appreciated 8.8 years ago, created a post with more than 5 votes. For Cuda/Gpu Processing And Bioinformatics
Good Question 8.8 years ago, asked a question that was upvoted at least 5 times. For Cuda/Gpu Processing And Bioinformatics
Popular Question 8.8 years ago, created a question with more than 1,000 views. For Cuda/Gpu Processing And Bioinformatics
Student 8.8 years ago, asked a question with at least 3 up-votes. For Cuda/Gpu Processing And Bioinformatics

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