User: jing.mengrabbit

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Posts by jing.mengrabbit

<prev • 20 results • page 1 of 2 • next >
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Comment: C: how to use the option of --rf and the options of -a and -a -a (-aa) in samtools
... Thanks for your time. The following is the reply from samtools developers about the difference between -a and -a -a (-aa): -a and -aa is all vs absolutely all (bad term I know). The difference is to do with references with zero coverage. For example if we have a file with @SQ headers for all chro ...
written 5 days ago by jing.mengrabbit0
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Comment: C: how to use the option of --rf and the options of -a and -a -a (-aa) in samtools
... Thanks for your time. The following is the reply from samtools developers about the difference between -a and -a -a (-aa): -a and -aa is all vs absolutely all (bad term I know). The difference is to do with references with zero coverage. For example if we have a file with @SQ headers for all chro ...
written 5 days ago by jing.mengrabbit0
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Comment: C: how to use the option of --rf and the options of -a and -a -a (-aa) in samtools
... Thanks Kevin for your answer. Do you know what is the difference between -a and -a -a (-aa)? ...
written 6 days ago by jing.mengrabbit0
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how to find the overlapping genomic sites for two big mpileup files and make a window file around these overlapping sites
... I have two mpileup files generated by samtools, their sizes are larger than 10GB. I would like to choose the genomic sites that are present in both mpileup files, and generate a matrix file. The matrix file has 201 columns, and the columns contain mpileup information for the genomic sites of overlap ...
genome sequence alignment written 8 days ago by jing.mengrabbit0
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how to use the option of --rf and the options of -a and -a -a (-aa) in samtools mpileup
... I am now using samtools (1.3.1-33) mpileup to create mpileup files, and would like to remove reads that have flags of 4, 8, 256, 512 and 1024. So should the --rf be set to 1804 (4+8+256+512+1024) or the --ff set to 1804? Also, what is the difference between options of -a and -a -a (-aa)? Thanks you! ...
genome sequence written 9 days ago by jing.mengrabbit0 • updated 6 days ago by Kevin Blighe13k
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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 months 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 months ago by jing.mengrabbit0 • updated 4 months ago by Alex Reynolds22k
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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 7 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 7 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 7 months ago by jing.mengrabbit0

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