file bed

[pingu]

Hello! I have a manifest file from Illumina and I would like to extract bed file. In the manifest file the targets have a strand + o - and in the file bed I would like to specify they, I see that it is possible but it is necessary to include the fields of ''name'' and ''score'', I do not know the field of score.
Thank you very much in advance

best regards

[Jessica_L]

Hi pingu,

Unless I'm mistaken (and someone please correct me if I'm wrong), the "score" field is only appropriate when working with actual data and really only affects the way those data are displayed in a browser such as UCSC. I believe the "strand" setting is similar-- it affects how data are displayed in a track (i.e. whether the read arrow points right or left). Depending on what you plan on using the .bed file for, that may or may not make sense to specify in your own file.

For a .bed file generated from a manifest, you won't really have a score for that since it wasn't based on data you generated. If you want to specify the strand of the DNA in the .bed file generated from the manifest, you may just be able to assign an arbitrary value, such as 1000, to the score for each line in the manifest and see if that suits your needs.

On the other hand, if you're just planning on using this .bed file as a reference, the "strand" field may not even be necessary, so you might be able to skip everything after the "Name" field. In other words, if the "score" and "strand" fields are for displaying track lines in a browser, it may not make sense to specify them if you're using the bed file as a reference for other purposes (i.e. if you're doing a vcf-bed intersect using vcflib tools).