convert junctions.bed to .juncs

[xy6699]

Hi,

Did anyone try the script " bed_to_juncs" supplied by tophat to convert junctions.bed to .juncs file ?

I have run: bed_to_juncs junctions.bed new_list.juncs,
but it's still running after two days!!! There is no error coming out.

After I forced it to stop by typing ^C, the following message came out:
^CTraceback (most recent call last):
File "/tophat-1.3.3/src/bed_to_juncs", line 68, in <module>
sys.exit(main())
File "/tophat-1.3.3/src/bed_to_juncs", line 43, in main
for line in sys.stdin.readlines():
KeyboardInterrupt

My junctions.bed has 26630 lines. Is it normal to take such a long time? What's the problem?

Many thanks for the help!

[craigb]

I know it's been a while but just in case anyone else hits this you need to pipe the inputs in and out of the script so you should run:

bed_to_juncs < junctions.bed > new_list.juncs

I found it threw an error about new_list.juncs being malformed but the file does get created.

[adumitri]

Hi craigb,

Thank you for your post - it was useful. I was wondering if you found out anything else about the warning message you mentioned:

Warning: malformed line 1, missing columns
	track name=junctions description="TopHat junctions"

The new_list.juncs output file looks fine for me, but just wanted to make sure nothing was wrong with it.

Alexandra

[craigb]

I didn't look into it anymore at the time, but looking at the warning message its not something to worry about.

The line "track name=junctions description="TopHat junctions" is (I think) just used by genome browsers to add extra display information, so if you're trying to get the juncs file that information wouldn't be of any use there.

HTH

Craig