I am using the blockbuster.x to do peak analysis, where it needs bed file as input. However, when I used one of my bed file, the blockbuster.x returned an error, saying that it's wrong file format. I don't understand why this is and I appreciate your help.
The first few lines of that bed is like this:
NC_012920.1 0 25 tag_22 1.0 -
NC_012920.1 0 26 tag_20 1.0 -
NC_012920.1 0 27 tag_18 1.0 -
NC_012920.1 0 28 tag_21 1.0 -
NC_012920.1 0 35 tag_17 2.0 -
NC_012920.1 0 37 tag_19 2.0 -
NC_012920.1 1 37 tag_24 1.0 -
NC_012920.1 4 23 tag_30 1.0 -
NC_012920.1 4 41 tag_32 1.0 -
NC_012920.1 4 42 tag_31 2.0 -
I think it's just a normal bed file?
it's not a bed file. https://genome.ucsc.edu/FAQ/FAQformat.html#format1
The first three required BED fields are: chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671). chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0. chromEnd - The ending position of the feature in the chromosome or scaffold.
Chromosome names can be anything; there are no particular rules for their names in the specification, only suggestions and examples.
Use head foo.bed | cat -te to verify that the input is tab-delimited and has Unix line endings. Use BEDOPS sort-bed foo.bed > foo.sorted.bed to ensure it is sorted, assuming your analysis tool requires sorted BED input.
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Are those blank lines bewteen the entries there in the actaul file, or are they a consequence of the way you've pasted it into biostars? Because they would almost certainly cause a problem if they are in the bedfile.