error to tabix bed file

Question

[cristina_sabiers]

Hi! Im back! XD didnt have so much time lately

I made an excel file with chr, and chrmstart-end and gen name like this

chr1    11873   14409   DDX11L1

chr1    14361   29370   WASH7P

chr1    17368   17436   MIR6859-1

chr1    17368   17436   MIR6859-2

chr1    17368   17436   MIR6859-3

chr1    17368   17436   MIR6859-4

chr1    30365   30503   MIR1302-2

chr1    30365   30503   MIR1302-9

chr1    30365   30503   MIR1302-10

chr1    30365   30503   MIR1302-11

chr1    34610   36081   FAM138A
......

I rename my xls file to bed, then I zip the file with this command

bgzip gen.bed

and when I try to tabbix I get this error message

tabix -p bed gen.bed.gz
[E::get_intv] failed to parse TBX_GENERIC, was wrong -p [type] used?
The offending line was: "��ࡱ�"
Segmentation fault (core dumped)

what I do wrong?

Thanks!

Answer 1

[Pierre Lindenbaum]

I think you saved your file as a native excel file. (show me the output of

$ file gen.bed

) There is no magic: nothing is changed by just hanging the suffix for xls to bed .

Sort on chr/start, export the file as CSV/TSV using tab as delimiter and no "escape string". Change the suffix from csv to bed. compress with bgzip and index with tabix.

[cristina_sabiers]

thanks Pierre!

I was misunderstanding I could just rename my xls file

Answer 2

[GenoMax]

Make sure you save the file as tab-delimited text out of Excel (which would make it BED format). You can't use xls formatted file as is.

[cristina_sabiers]

thanks

then I read wrong , I could just rename it.... ^^"