Fwd: Invalid signed integer question

[Jeremy Johnson]

Hi guys,

I'm trying to update a track on our track hub, but before doing that I'm trying to simply upload a bed (or even a single line) of data to QC it.

However, I keep getting the "invalid signed integer:+[weird diamond with question mark character]" error (including from a separate BED file that I know previously worked.)  I have a screenshot, but can't send it along to this address.  I can send it to whoever takes on this particular request.

I've checked, and there is no scientific notation in my file, and I've made sure that any formatting is stripped out.  I've tried it both tab-separated and single-white space character separated to no avail.  I've copied below a sample from the files I'm using that gives me the error.

Any help is greatly appreciated!

~Jeremy

Jeremy Johnson
Project Coordinator
Vertebrate Biology Group
Broad Institute

Tel:  (617) 714-7935

chr1    247828    322180    ENPP1    1000    -    247828    322180    55,126,184    25    4734,163,133,81,130,155,52,170,88,70,128,32,132,109,73,66,110,120,80,98,61,126,117,73,330    0,6637,8368,9333,14005,15695,17749,18630,20422,21237,22655,23936,25736,28089,30416,30799,31766,32941,34065,36033,38075,39013,39958,41845,74022    5250
chr1    247828    322180    ENPP1    1000    -    247828    322180    55,126,184    25    4734,163,133,81,130,155,52,170,88,70,128,32,132,109,47,66,110,120,80,98,61,126,117,73,330    0,6637,8368,9333,14005,15695,17749,18630,20422,21237,22655,23936,25736,28089,30416,30799,31766,32941,34065,36033,38075,39013,39958,41845,74022    5249
chr1    247828    322180    ENPP1    1000    -    247828    322180    55,126,184    24    4734,163,133,81,130,155,52,170,88,70,128,32,132,109,73,66,110,120,98,61,126,117,73,330    0,6637,8368,9333,14005,15695,17749,18630,20422,21237,22655,23936,25736,28089,30416,30799,31766,32941,36033,38075,39013,39958,41845,74022    5248
chr1    261585    273988    ENPP1    1000    -    261585    273988    55,126,184    9    378,155,52,170,88,70,128,32,424    0,1938,3992,4873,6665,7480,8898,10179,11979    5251
chr1    270004    275409    ENSCAFG00000030108    1000    +    270004    275409    55,126,184    2    105,861    0,4544    1

[Steve Heitner]

Hello, Jeremy.

I can’t speak for your other bed files that previously worked and are now not working, but at least for the snippet of data you sent, the bed data contains 13 columns of data (the 13^th column contains the values “5250”, “5249”, “5248”, “5251”, “1”).  When I loaded the data as is, I saw the same error you were seeing.  When I removed the 13^th column, the custom track loaded just fine.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  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.

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Steve Heitner
UCSC Genome Bioinformatics Group

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