[Genome] request for hg18 to hg16
Brooke Rhead
rhead at soe.ucsc.edu
Sun Apr 6 11:57:03 PDT 2008
Hi Ashutosh,
You can run all of the commands in your text file by making the file
executable:
chmod +x textfile
If the file is in your current working directory, you can run it like this:
./textfile
(If it's not in your current directory, you will need to give the path
to it, like you did for the liftOver command.)
--
Brooke Rhead
UCSC Genome Bioinformatics Group
Hiram Clawson wrote:
> Good Morning Ashutosh:
>
> You can download a binary for the Mac from the location:
> http://hgdownload.cse.ucsc.edu/admin/exe/
> although this is a PPC binary only, not an Intel binary.
>
> This is merely the program, it is not a Mac dmg packaged
> object. Simply set the execution bits on with a 'chmod'
> then run the binary from a command line. It will output
> its usage message when run with no arguments.
>
> --Hiram
>
> Gupta, Ashutosh (NIH/NCI) [F] wrote:
>> Thanks a lot Ann for the quick reply! It was very helpful.
>> I had read the details for BED format, but didn't realize that optional
>> arguments also had a format.
>>
>> The problem with adding all the data to new.tsv file is that each file
>> is about 50 MB, so adding all the files to one file (~3 GB) would take
>> for ever & then conversion might be another forever.
>>
>> The easiest way around it seems to be the following.
>> I can write a text file with all the conversion commands, e.g.
>> liftOver file1 chainFile newFile1 unMapped1
>> liftOver file2 chainFile newFile2 unMapped2
>> ...
>> liftOver file150 chainFile newFile150 unMapped150
>>
>> And than run that text file from terminal server on the Mac.
>>
>> Question is: How do I run it from terminal server?
>>
>> Thanks a lot for all the help.
>> Best regards,
>> Ashutosh.
>>
>>
>> -----Original Message-----
>> From: Ann Zweig [mailto:ann at soe.ucsc.edu]
>> Sent: Thursday, April 03, 2008 5:09 PM
>> To: Gupta, Ashutosh (NIH/NCI) [F]
>> Cc: 'genome at soe.ucsc.edu'
>> Subject: Re: RE: [Genome] request for hg18 to hg16
>>
>> Hello Ashutosh,
>>
>> Please note that our mail list software strips all attachments
>> sent to the
>> list. That said, I was able to deduce what is happening with your input
>> files.
>>
>> The scores that you have entered in your input file are in the
>> 6th field. They
>> must be moved to the 5th field. The 6th field is reserved for strand
>> (+/-).
>> Please read about the BED format here:
>> http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
>>
>> You should be able to run all of your conversions at one time.
>> Just place them
>> all in your new.tsv file and run it as Brooke explained previously.
>>
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>> Please feel free to search the Genome mailing list archives by visiting
>> our home
>> page, clicking on "Contact Us", then typing a word or phrase into the
>> search
>> box. On that same page
>> (http://genome.ucsc.edu/contacts.html), you can subscribe to the Genome
>> mailing
>> list.
>>
>>
>>
>>> Hey Brooke,
>>>
>>> Thanks a lot for the help.
>>>
>>> It did work. However I had to use the same strategy as earlier (that
>> is
>>> to give the complete path).
>>>
>>> I could not find the $PATH directories to copy my files over there.
>>>
>>>
>>>
>>> But problem is, that the data values were changed.
>>>
>>> This is before conversion:
>>>
>>> This is after conversion:
>>>
>>>
>>>
>>> Note the special characters & changed score values in the last column.
>>>
>>>
>>>
>>> Exactly the same thing happened when I was using the web version of
>> the
>>> liftOver program.
>>>
>>> How to fix this? I could just take the coordinates from the shifted
>>> file, & scores from the original file, would it be correct to do so?
>>>
>>>
>>>
>>> Also is there a way to run a lot of these liftOver commands at one go?
>> I
>>> need to run about 150 conversions, doing them one by one will take
>>> forever. If I can write all the commands in a single text file, how do
>> I
>>> execute that file Mac?
>>>
>>>
>>>
>>> Thank you so much for your help. I really appreciate it.
>>>
>>>
>>>
>>> Regards,
>>>
>>> Ashutosh.
>>>
>>> PS: In case you can't see the embedded pictures in this email, I have
>>> attached a copy of this email in the pdf format too.
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Brooke Rhead [mailto:rhead at soe.ucsc.edu]
>>> Sent: Wednesday, April 02, 2008 3:15 AM
>>> To: Gupta, Ashutosh (NIH/NCI) [F]
>>> Cc: genome at soe.ucsc.edu
>>> Subject: Re: [Genome] request for hg18 to hg16
>>>
>>>
>>>
>>> Hi Ashutosh,
>>>
>>>
>>>
>>> I see these lines in your attached file:
>>>
>>>
>>>
>>> nci-admins-computer-2:~ levensd$
>>>
>>> /Volumes/nci10b.nci.nih.gov/Group/LP/Ashutosh/HG\ liftover/liftOver
>>>
>>> new.tsv hg17ToHg16.over.chain ne2 unMapped
>>>
>>> Can't find file: new.tsv
>>>
>>> nci-admins-computer-2:~ levensd$
>>>
>>> /Volumes/nci10b.nci.nih.gov/Group/LP/Ashutosh/HG\ liftover/liftOver
>>>
>>> new.tsv hg17ToHg16.over.chain ne2 unMapped
>>>
>>> Can't find file: new.tsv
>>>
>>> nci-admins-computer-2:~ levensd$
>>>
>>> /Volumes/nci10b.nci.nih.gov/Group/LP/Ashutosh/HG\ liftover/liftOver
>> new
>>> hg17ToHg16.over.chain ne2 unMapped
>>>
>>> Can't find file: new
>>>
>>> nci-admins-computer-2:~ levensd$
>>>
>>> /Volumes/nci10b.nci.nih.gov/Group/LP/Ashutosh/HG\ liftover/liftOver
>>>
>>> new.tsv hg17ToHg16.over.chain ne2 unMapped
>>>
>>> Can't find file: new.tsv
>>>
>>> nci-admins-computer-2:~ levensd$
>>>
>>> /Volumes/nci10b.nci.nih.gov/Group/LP/Ashutosh/HG\ liftover/liftOver
>>>
>>> new.txt hg17ToHg16.over.chain ne2.txt unMapped
>>>
>>> Can't find file: new.txt
>>>
>>> nci-admins-computer-2:~ levensd$ \306\222f
>>>
>>>
>>>
>>>
>>>
>>> For comparison, the format for running the liftOver command is:
>>>
>>>
>>>
>>> liftOver oldFile map.chain newFile unMapped
>>>
>>>
>>>
>>> The first two files, "oldFile" and "map.chain" need to either be
>> present
>>> in your current working directory, or else you need to specify the
>> paths
>>> to the files. The second two files, "newFile" and "unMapped" do not
>>>
>>> need to exist already -- the liftOver program will create files with
>> the
>>> names you specify.
>>>
>>>
>>>
>>> Using your command:
>>>
>>> liftOver new.tsv hg17ToHg16.over.chain ne2 unMapped
>>>
>>>
>>>
>>> liftOver is expecting a BED file of hg17 coordinates in to be present
>> in
>>> the current directory, in a file called "new.tsv". The
>>>
>>> hg17ToHg16.over.chain file should also be in the current directory.
>>>
>>> LiftOver will create a file containing the corresponding hg16
>>>
>>> coordinates in a file called "ne2" in the current directory, and it
>> will
>>> create a file called "unMapped" in the current directory and record
>> any
>>> hg17 coordinates that did not map to hg16 in that file.
>>>
>>>
>>>
>>> Regarding your "PS" question: I see that you presently need to specify
>>>
>>> the entire path to the liftOver executable to get it to work. This is
>>>
>>> because the path to liftOver is not in your $PATH variable. If you
>>>
>>> either (1) move the liftOver executable to a directory that is already
>>>
>>> in $PATH, or if you (2) add the path where your executable resides
>>>
>>> (/Volumes/... in your case) to the $PATH variable, you should be able
>> to
>>> execute liftOver without specifying the path to it every time. Try
>> the
>>> command:
>>>
>>> echo $PATH
>>>
>>> to see the directories that are currently in your $PATH variable.
>>>
>>>
>>>
>>> I hope this explanation is helpful.
>>>
>>>
>>>
>>> --
>>>
>>> Brooke Rhead
>>>
>>> UCSC Genome Bioinformatics Group
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Gupta, Ashutosh (NIH/NCI) [F] wrote:
>>>
>>>> Thanks a lot for the quick reply.
>>>> Please have a look at the attached snapshot of my liftOver session.
>>>> I am not sure where am I going wrong. I have tried several different
>>>> formats, but the program never recognized the files. The files were
>>>> definitely there as I could open them using other applications.
>>>> I had also ensured that the data is in the recommended BED format.
>>>> Thanks again for your help.
>>>> Regards,
>>>> Ashutosh.
>>>> PS: Also, I notice that you are just typing liftOver from the
>> command
>>>> promt, which never worked for me. I always got the error-"command
>> not
>>>> found". So I had to use the strategy as in the attached file. Is
>> there
>>>> some problem with the installation of the file? I am a windows user
>> &
>>>> relatively new to mac/unix system.
>>>> -----Original Message-----
>>>> From: Brooke Rhead [mailto:rhead at soe.ucsc.edu]
>>>> Sent: Tuesday, April 01, 2008 8:30 PM
>>>> To: Gupta, Ashutosh (NIH/NCI) [F]
>>>> Cc: genome at soe.ucsc.edu
>>>> Subject: Re: [Genome] request for hg18 to hg16
>>>> Hi Ashutosh,
>>>> What kind of problem are you experiencing?
>>>> If you just need instructions on how to use the command-line tool,
>> you
>>>> can run the liftOver command with no arguments to see instructions.
>> It
>>>> should look something like this:
>>>> -----
>>>> $ liftOver
>>>> liftOver - Move annotations from one assembly to another
>>>> usage:
>>>> liftOver oldFile map.chain newFile unMapped
>>>> oldFile and newFile are in bed format by default, but can be in GFF
>> and
>>>> maybe eventually others with the appropriate flags below.
>>>> The map.chain file has the old genome as the target and the new
>> genome
>>>> as the query.
>> ***********************************************************************
>>>> WARNING: liftOver was only designed to work between different
>>>> assemblies of the same organism, it may not do what you
>> want
>>>> if you are lifting between different organisms.
>> ***********************************************************************
>>>> options:
>>>> -minMatch=0.N Minimum ratio of bases that must remap. Default
>> 0.95
>>>> -gff File is in gff/gtf format. Note that the gff lines are
>>>> converted
>>>> separately. It would be good to have a separate check
>> after
>>>> this
>>>> that the lines that make up a gene model still make a
>>>> plausible gene
>>>> after liftOver
>>>> -genePred - File is in genePred format
>>>> -sample - File is in sample format
>>>> -bedPlus=N - File is bed N+ format
>>>> -positions - File is in browser "position" format
>>>> -hasBin - File has bin value (used only with -bedPlus)
>>>> -tab - Separate by tabs rather than space (used only with
>> -bedPlus)
>>>> -pslT - File is in psl format, map target side only
>>>> -minBlocks=0.N Minimum ratio of alignment blocks/exons that must
>> map
>>>> (default 1.00)
>>>> -fudgeThick If thickStart/thickEnd is not mapped, use the
>> closest
>>>> mapped base. Recommended if using -minBlocks.
>>>> -multiple Allow multiple output regions
>>>> -minChainT, -minChainQ Minimum chain size in target/query, when
>>>> mapping
>>>> to multiple output regions (default 0, 0)
>>>> -minSizeT deprecated synonym for -minChainT (ENCODE
>>>> compat.)
>>>> -minSizeQ Min matching region size in query with
>>>> -multiple.
>>>> -chainTable Used with -multiple, format is
>> db.tablename,
>>>> to extend chains from net (preserves
>>>> dups)
>>>> -errorHelp Explain error messages
>>>> -----
>>>> If you are only converting 50 positions from hg18 to hg16, it might
>> be
>>>> easier to use the web-based tool, as Kayla suggested. (Or did I
>>>> misunderstand your original question, and you need to convert many
>> more
>>>> than 50 positions?)
>>>> --
>>>> Brooke Rhead
>>>> UCSC Genome Bioinformatics Group
>>>> Gupta, Ashutosh (NIH/NCI) [F] wrote:
>>>>
>>>>> Hi,
>>>>> I am having problem with conversions across different builds.
>>>>> I have the liftOver tool for Mac OS X & all the relevant chain
>> files.
>>>>> Any help on this would be appreciated.
>>>>> Thanks,
>>>>> Ashutosh.
>>>>> -----Original Message-----
>>>>> From: Kayla Smith [mailto:kayla at soe.ucsc.edu]
>>>>> Sent: Monday, March 24, 2008 5:15 PM
>>>>> To: Gupta, Ashutosh (NIH/NCI) [F]
>>>>> Cc: genome at soe.ucsc.edu
>>>>> Subject: Re: [Genome] request for hg18 to hg16
>>>>> Hello Ashutosh,
>>>>> You can use our online liftOver tool to convert from hg18 to hg17,
>> and
>>>>>
>>>>
>>>>> then from hg17 to hg16. Here is the link:
>>>>> http://genome.ucsc.edu/cgi-bin/hgLiftOver
>>>>> See this FAQ on downloading our source:
>>>>> http://genome.ucsc.edu/FAQ/FAQdownloads#download27
>>>>> I hope this information is helpful to you. Please don't hesitate
>> to
>>>>> contact us again if you require further assistance.
>>>>> Kayla Smith
>>>>> UCSC Genome Bioinformatics Group
>>>>> Gupta, Ashutosh (NIH/NCI) [F] wrote:
>>>>>
>>>>>> Hi,
>>>>>> Would it be possible to get a liftover file for conversion from
>> hg18
>>>>>>
>>>>> to
>>>>>
>>>>>> hg16?
>>>>>> Also, is there any windows based conversion mechanism? I need to
>>>>>>
>>>>> convert
>>>>>
>>>>>> about 50 nimblegen encode array hybridization, a windows based
>> tool
>>>>>> would be very helpful.
>>>>>> Even the conversion source code in C (or in Mathematica or Matlab)
>>>>>>
>>>>> would
>>>>>
>>>>>> be very helpful.
>>>>>> Thanks,
>>>>>> Ashutosh.
>>>>>> PS: I can also help develop a tool for windows system, depends on
>>>>>> complexity & time though. I am sure a lot of people would find it
>>>>>> useful.
>>>>>> _______________________________________________
>>>>>> Genome maillist - Genome at soe.ucsc.edu
>>>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>>>>>
>>>>> _______________________________________________
>>>>> Genome maillist - Genome at soe.ucsc.edu
>>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>>>>
>>>
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>>
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> http://www.soe.ucsc.edu/mailman/listinfo/genome
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