Error parsing line at byte position: htsjdk.tribble.readers .bed

[Ashwin Venkateshvaran]

Hi, i am trying to use IGV to generate a linear gene plot and when i use a template file(which is my colleague's) it works like a charm. But when i try to feed my own file into the system (which is based on his format exactly) i recieve an error of which i've attached as a screenshot below. Basically I input my data in an excel file and save it as tab de-limited with a .BED extension and feed it to the software and get this error. And ive also notice that when i try and create a copy of his file(my colleague's), as in save it under a different name under the same format, the same error comes up. Any help would be highly appreciated.

[Jim Robinson]

Hi well need to see a sample file that reproduces the problem.   Also, what version of igv are you using?

Hi, i am trying to use IGV to generate a linear gene plot and when i use a template file(which is my colleague's) it works like a charm. But when i try to feed my own file into the system (which is based on his format exactly) i recieve an error of which i've attached as a screenshot below. Basically I input my data in an excel file and save it as tab de-limited with a .BED extension and feed it to the software and get this error. And ive also notice that when i try and create a copy of his file(my colleague's), as in save it under a different name under the same format, the same error comes up. Any help would be highly appreciated.

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[Ashwin Venkateshvaran]

Its version 2.3.40 and ive attached a sample below, im not able to figure where the format has gone wrong or why its not parsing. Thank so much for the help

[Jim Robinson]

Hi, you just need to remove the quotes surrounding the first line (the track line).

Jim

Its version 2.3.40 and ive attached a sample below, im not able to figure where the format has gone wrong or why its not parsing. Thank so much for the help

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[arieh....@gmail.com]

Arieh:  See ScreenShot for error downloading a bed file on the IGV browser

In this case I generated a bed file in R and apparently R convert automatically an integer position to scientific notation: so 38000000 becomes 3.8e+7 in the bed file.

Good luck, Arieh

Op zondag 8 februari 2015 06:12:58 UTC+1 schreef Ashwin Venkateshvaran: