how many columns does F-seq need in the bed file

Question

[Shaway]

recently, I using F-seq to run some DNase-seq data.

I know F-seq need bed file as input, so I merged my paired end sequence and got a bed file contain 5 column like below:

chr10 29334602 29334656 SRR891270.293 255

chr10 61751512 61751575 SRR891270.256 255

chr10 103211892 103212065 SRR891270.153 255

the unmerged data are as follows: chr10 29334602 29334652 SRR891270.293/2 255 +

chr10 29334606 29334656 SRR891270.293/1 255 -

chr10 61751512 61751562 SRR891270.256/2 255 +

chr10 61751525 61751575 SRR891270.256/1 255 -

chr10 103211892 103211942 SRR891270.153/2 255 +

chr10 103212015 103212065 SRR891270.153/1 255 -

I thinks the merged data should be the input file for F-seq, does anybody know how many columns F-seq need? 3 or 5 columns enough?

thanks!

Answer 1

[spacemorrissey]

All F-seq really needs is the chrome, start position, and strand, but it expects to find that in bed format. So you should send it a file with 6 columns as below. Columns 4 and 5 are ignored, so you can put what ever you want in there. Also, since F-seq works on the density of cut sites, not an overlap of fragments, it really doesn't matter what the end position is, so you can make the end position the start position plus one.

1 2 3 4 5 6

chr7 131441220 131441240 DGM97JN1_120416_0202_AD0F2LABXX:2:1101:1463:2096#0/1 . + chr19 37087535 37087555 DGM97JN1_120416_0202_AD0F2LABXX:2:1101:1420:2094#0/1 . - chr7 126871377 126871397 DGM97JN1_120416_0202_AD0F2LABXX:2:1101:1479:2133#0/1 . - chr12 19418187 19418207 DGM97JN1_120416_0202_AD0F2LABXX:2:1101:1335:2100#0/1 . - chr5 118422430 118422450 DGM97JN1_120416_0202_AD0F2LABXX:2:1101:1342:2124#0/1 . -

[spacemorrissey]

Oops the text editor wrapped the lines of data. Just give it:

Chrom start stop . . strand