User: jing.mengrabbit

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Posts by jing.mengrabbit

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Comment: C: identify the type of repeat genomic region of a BED file
... Thank you. I'll give this a shot. ...
written 4 weeks ago by jing.mengrabbit0
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identify the type of repeat genomic region of a BED file
... Hi, I have a BED file containing different human genomic regions. I would like to know if these genomic regions belong to repeat regions, and what type of repeat regions they belong to, such as Microsatellite, Minisatellite, LINES, SINES, etc. Is there a tool that can do the task? Thanks! ...
genome sequence written 4 weeks ago by jing.mengrabbit0 • updated 4 weeks ago by Alex Reynolds21k
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Comment: C: multiprocesses vs multithreads in application
... Thank you. Where can I see the number of threads? by which command? ...
written 4 months ago by jing.mengrabbit0
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Comment: C: multiprocesses vs multithreads in application
... Why we do not need to worry about allocating threads in linux? Can linux adjust the resource allocation automatically? ...
written 4 months ago by jing.mengrabbit0
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Comment: C: multiprocesses vs multithreads in application
... So Does it mean that both commands each use 4 CPUs or what? ...
written 4 months ago by jing.mengrabbit0
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Comment: C: multiprocesses vs multithreads in application
... Thanks for your advice. I will follow it. ...
written 4 months ago by jing.mengrabbit0
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Comment: A: multiprocesses vs multithreads in application
... Thanks for all your reply. I understand the concepts thread, processor and process now. The application I am using is working on an BAM file, doing a series of analysis on each site. These series of analysis on each site are performed by 3rd party tools (samtools, bedtools ....) plus functions writ ...
written 4 months ago by jing.mengrabbit0
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Comment: C: multiprocesses vs multithreads in application
... Thanks Alex. From the application's documentation, there is no multi-threads option. I'd better check with the developer. An application supporting multi-processes does not necessarily support multi-cores, does it? And for the multi-processes option, will the application be quicker with -p 3 than ...
written 4 months ago by jing.mengrabbit0
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multiprocesses vs multithreads in application
... Hi, I know little about writing a tool. Sorry if my question is too obvious. I am still confused after google search . I know that selecting the same number of cores that an application (assuming there are enough cores available on the machine) can support will get the application running at its ...
software error written 4 months ago by jing.mengrabbit0
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BAMSurgeon error report: bam readcount < fastq readcount, alignment sanity check failed!
... Hi, I ran BAMSurgeon (https://github.com/adamewing/bamsurgeon), and it gives the following error report: ERROR 2017-07-06 09:03:39.934250 encountered error in mutation spikein: ['chr1_27691816_27691816_0.5_None'] Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-pac ...
software error genome written 4 months ago by jing.mengrabbit0

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