User: Amirosein

gravatar for Amirosein
Amirosein70
Reputation:
70
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Trusted
Location:
UBC, Vancouver, CA.
Last seen:
3 months ago
Joined:
2 years, 11 months ago
Email:
a***********@gmail.com

Posts by Amirosein

<prev • 40 results • page 1 of 4 • next >
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Comment: C: parallel bwa mem with compressed fastq.bz2 files
... Thanks for your COMPLETE reply, yeah I was answering fast and I missed some of the points. Thanks for pointing out. and I have to add that the machine has more than 44 cores. Thanks again. ...
written 3 months ago by Amirosein70
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Comment: C: parallel bwa mem with compressed fastq.bz2 files
... Thank, but I am wondering what is wrong with my code! If there is no problem then the code you provided will be slower than mine, as you are doing both the things separately. Theoretically, if you use piping you are not going to be slower at least...! And my problem is that I want to be faster and ...
written 3 months ago by Amirosein70
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Comment: C: parallel bwa mem with compressed fastq.bz2 files
... But it is not using all the 20 cores! yeah I am looking at CPU usage but it is totally different from when you pass an uncompressed file into it... ...
written 3 months ago by Amirosein70
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parallel bwa mem with compressed fastq.bz2 files
... Hi all, I have a set of 2 compressed paired files like: L1_R1.fastq.bz2 L1_R2.fastq.bz2 and I want to run `bwa mem` with multiple threads on it. As the files are compress in `.bzip2` I am using a shell script to pipe two commands for compressing both into `bwa mem` at once. The code is a ...
bzip2 bwa-mem linux bwa bash written 3 months ago by Amirosein70
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Comment: C: is there any fast and accurate read mapper which provides and easy-to-use API?
... Blat of DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. mentioned in BLAT documentation. ...
written 12 months ago by Amirosein70
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Comment: C: is there any fast and accurate read mapper which provides and easy-to-use API?
... Yeah, but unfortunately it is not for bwa-aln. In my case, I should use bwa-aln. ...
written 12 months ago by Amirosein70
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Comment: C: is there any fast and accurate read mapper which provides and easy-to-use API?
... yeah but regardless of if they are the best option, short-reads are reads of length ~100-200 bps. here I want to align substrings of reads of length 25. ...
written 12 months ago by Amirosein70
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Comment: C: is there any fast and accurate read mapper which provides and easy-to-use API?
... thank you for your reply, but it's not. it is good for long reads of nanopore or pacbio technology. The best one is bwa-aln from the same author but it does not provide easy to use API. you can see the instructions from one of the contributors in my updated post. ...
written 12 months ago by Amirosein70
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Comment: C: is there any fast and accurate read mapper which provides and easy-to-use API?
... Thanks a lot. seems good. I'll check it in detail. ...
written 12 months ago by Amirosein70
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Comment: C: is there any fast and accurate read mapper which provides and easy-to-use API?
... Aha, good idea, but it will be more useful if we can find a read mapper with an API. Thank you for your idea and consideration. ...
written 12 months ago by Amirosein70

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Popular Question 3 months ago, created a question with more than 1,000 views. For detection of in/del in sanger sequencing
Popular Question 11 months ago, created a question with more than 1,000 views. For importing .SAM files into R (Rstudio)
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Scholar 2.8 years ago, created an answer that has been accepted. For A: Retrieving overlaps inside a single dataset using foverlaps

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