Unlocalized contig visualisation and filtration for bed files.
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7.4 years ago
morovatunc ▴ 550


I have couple questions related to bed file analysis and we have unlocalised regions in our bed file after the overlapping bed regions analysis.

1) I know I can write a script that will eliminate everything but chr1-2-3-4... would it be a smart idea ? ( I am totally interested in known regions) Also, Can this be the lack of mappability of hg19 ? Should I try grch38 ?

2) If it is possible how can I visualise these regions in IGV ? 3) In couple of the chr3-4-5 regions, we have observed that NNNNNNNNNNNNNN sequence in present. It is probably a sequencing error. I would like to know, if those repeating regions are kept in a document so that I can make a filtration that will eliminate those regions and give me the most confident results?

For example, assume following regions are found to be repeating or NNNNNNNNNNNN and there is list of these intervals so that I can eliminate from my bed file before I find my overlaps.

chr1 100 2500 chr1 5000 6200

Thank you very much,



a sample from my overlaps.

chrKI270466.1   637 902 89.867126
chrKI270438.1   111985  112321  82.382042
chrKI270733.1   158634  158781  80.990242
chrKI270438.1   109559  109720  77.981293
chrGL000220.1   138579  138817  56.679230
chrGL000225.1   50760   50972   47.351170
chrGL000225.1   67365   67555   35.525284
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