User: brs1111

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brs111110
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Posts by brs1111

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Comment: C: Faster reading sequences from a fastq file
... Thanks for your help !! Let me try these compiler flags. I will try to figure it out. ...
written 21 months ago by brs111110
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Comment: C: Faster reading sequences from a fastq file
... Yes, I saw that on ntCard paper. In fact, I used the sample code given in [ntHash][1] [1]: https://github.com/bcgsc/ntHash ...
written 21 months ago by brs111110
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Answer: A: De novo assembly
... spades (http://bioinf.spbau.ru/spades) might be a better option ...
written 21 months ago by brs111110
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Comment: C: Faster reading sequences from a fastq file
... Thanks for the suggestion. I modified the code and it works good now. It takes little more than an hour just to read and count the number sequences. But when I calculate hash for all k-mers of all sequences , it takes more than 7 hours. I understand that there are additional operations for calculati ...
written 21 months ago by brs111110
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Comment: C: Faster reading sequences from a fastq file
... Hi Chen, I am not able to figure out how to use it. Could you please provide a simple main() ? ...
written 22 months ago by brs111110
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Comment: C: Faster reading sequences from a fastq file
... Thanks Chen !! Let me try fastp ...
written 22 months ago by brs111110
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Comment: C: Faster reading sequences from a fastq file
... Yes, it is not compressed. ...
written 22 months ago by brs111110
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Comment: C: Faster reading sequences from a fastq file
... Thanks Alex for the suggestions. ...
written 22 months ago by brs111110
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Faster reading sequences from a fastq file
... I have a fastq file of size 450gb (162,266,303 sequences) and I would like to parse the sequences. I am using Heng Li's C program ([https://github.com/lh3/readfq][1]). I am wondering if it is the fastest one as it takes more than an hour to just count the number of sequences using the following prog ...
fastq C written 22 months ago by brs111110 • updated 22 months ago by kloetzl1.1k
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Answer: A: GeneMarkS error when it runs gmhmmp
... I think it is the license issue GeneMark.hmm 400-day license. Your 400-day license period has ended. We hope that you found this software useful. If you would like to renew this license, please contact GeneProbe, Inc. at custserv@genepro.com ...
written 2.1 years ago by brs111110

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