giggle index and search using the same file error

[Sita Zhou]

Hello, I encountered a really strange problem, 

I indexed my file of genomic regions, when I try to use the same file to perform search function, I got no error messages, but giggle stay in running status, without results return , is there self search restriction in giggle?

This is the command:

$giggle index -i test.bed.gz -s -o test_index

$giggle search -i test_index  -q test.bed.gz -s

Thank you in advance!

Sita

[Ryan Layer]

Try putting that file in a folder by itself, maybe “test”, then do -i “test/*.bed.gz”

--
You received this message because you are subscribed to the Google Groups "giggle" group.
To unsubscribe from this group and stop receiving emails from it, send an email to giggle-discus...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/giggle-discuss/bfa4dd14-b324-4514-a456-cfc530cb0584%40googlegroups.com.

[周瑶]

Thanks you for your reply!
Unexpected region overlaps exsit in my file, I solved this problem after using bedtools merge function.

Best,
Sita