[Genome] request for hg18 to hg16
Ann Zweig
ann at soe.ucsc.edu
Thu Apr 3 14:08:41 PDT 2008
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
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>
> 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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> confirm 4d79c0dc8c71eefc5082009115917a5d3cb4ff34
> From:
> genome-request at soe.ucsc.edu
>
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