Hi David,
You didn't use samtools, you used the system sort command instead. You
must fully type "samtools sort" at the beginning of the command to use
samtools.
Devon
On 08/15/2016 09:58 PM, David Siegel wrote:
Greetings
I've installed Samtools successfully on my Mac (downloaded the file,
unpacked it, cd'd into the folder, typed "make" on the command line,
tested it on a SAM file, and it worked fine). The command I'm using
is: sort -n --output testfile_sorted_aligned
~/Documents/blahblahAligned.out.sam
I also installed it onto my work cluster (a unix-based environment),
and it worked ok but had a weird bug: It sorted the header file
alphabetically in addition to the mapped SAM data. So some of the
header data now comes at the end of the file, some of it comes at the
beginning.
If this is really the only issue I can always just write code to get
around it. But if it's a common symptom of some sort of error in
installation, could someone let me know how to fix it?
I'm also not the most savvy individual when it comes to the unix/linux
environment, I've only been using it for a few months.
Thanks,
David
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Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dprya...@gmail.com
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
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