ERROR: reads not sorted while the reads are sorted

[julie]

Hi,

I cannot run the latest version of RSEG because it says me :

ERROR: reads not sorted in myBedfile.bed

chr1	3836344	3836381	2781376	0	-
chr1	3836344	3836381	440874	0	+

I began my analyse by a sorting with bedtools, and for me, this example in not unsorted.

Furthermore, this file was supported without error in the first version of RSEG.

How can I obtain a file which is supported by the new version of RSEG.

Thanks.

Julie

[Song, Qiang]

Hi Julie,

rseg sorting also use the strand info, i.e., + should precedes - if two reads have the same location.

To do the sorting, run

export LC_ALL=C

sort -k1,1 -k3,3n -k2,2n -k6,6 input.bed -o input-sorted.bed

Regards,

Song Qiang

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[julie]

Thanks a lot!
It works.

Julie