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how to get input file of closest-features a bed-format file

HI everyone!

i am trying to calculate the gene distance of assembly contigs by closest-features. but this tool requires a bed format input file. how can i get this bed-format file?

genome sequencing gene
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updated by jordi.planells jordi.planells • written by MEITUO • MEITUO

What kind of data do you have? Could you please share more details?

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written by jordi.planells jordi.planells

metagenic data, the contigs after assembly

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written by MEITUO • MEITUO

if you have the bam format you can use bedtools bamtobed (see here).

Then you can use bedtools closest (see here) to intersect the bed file obtained earlier with the features (also in bed). If you specify the -d flag, it will report the distance as well.

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written by jordi.planells jordi.planells

thanks! and is the bam file that the qc reads mapping back to assembly contig? do this need filter low mapped reads or just can use it directly after bwa or bowite??

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written by MEITUO • MEITUO

That I didn't get it sorry... Please explain better what you mean. If you have doubts about what a bam file is, you should spend some time familiarizing with the file types used in bioinformatics. See here for a short description of the most common file types in bioinformatics.

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written by jordi.planells jordi.planells

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