the bigPsl file by converting psl to bigPsl with current version of pslToBigPsl tool not bed 12+12

[Liu, Yating]

Hello,

I found that the new version of pslToBigPsl tool (v343, 17-Jan-2017 at http://hgdownload.soe.ucsc.edu/admin/exe/) will output the bigPsl file with an extra column (bed 12+13) instead of bed 12+12. However the document https://genome.ucsc.edu/goldenPath/help/bigPsl.html does not mention this new scheme. So I am wondering if you are going to use this new bigPsl format (bed 12+13) in UCSC genome browser and update the documentation? If so, will you still support the display of old bigPsl files (bed 12+12). 

Thank you!

Best,

Yating

[Chris Villarreal]

Dear Liu,

Thank you for your question about the UCSC Genome Browser tools. The pslToBigPsl tool was recently updated to include the extra column. The documentation has been updated but it should work with the old bigPsl files (bed 12+12).

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

-Chris V

UCSC Genome Browser

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser discussion list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.

[Liu, Yating]

Dear Chris,

Thank you for updating the documentation. While the bigpsl.as link has not been updated to the new version yet at https://genome.ucsc.edu/goldenPath/help/bigPsl.html, which is still 24 columns. 

In addition, the usage note when run psltobigpsl is still showing "-type=bed12+12". You may want to update that at http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/hg/utils/pslToBigPsl/pslToBigPsl.c;hb=1234f3ad8d68b1865c6010b29ae2d9ab488f54d5 in line 24: "   bedToBigBed -type=bed12+12 -tab -as=bigPsl.as file.bigPslInput chrom.sizes output.bb\n".

The first line of the code "/* pslToBigPsl - converts genePred or genePredExt to bigGenePred. */" is not for pslToBigPsl. 

Thank you!

Best,

Yating

---

From: Chris Villarreal <cjvi...@ucsc.edu>
Sent: Friday, January 20, 2017 2:50 PM
To: Liu, Yating
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] the bigPsl file by converting psl to bigPsl with current version of pslToBigPsl tool not bed 12+12

 

[Chris Villarreal]

Dear Yating,

Thank you for informing us about the bigPsl.as link which is now updated, https://genome.ucsc.edu/goldenPath/help/examples/bigPsl.as. The pslToBigPsl usage statement will be updated in our next release. I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

-Chris V
UCSC Genome Browser