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Finding specific k-mer in human genome

I want to find a specific 9-mer (GATCGATGC) in human genome, and then export them into a bed file with all information including chromosome, start and end position. A lot of tools such as jellyfish and DSK can only count k mer occurrence and can't export k mer information. Does anybody know how to do this? Any suggestion would be greatly appreciated.

k-mer bed list all coordinates
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updated by Alex Reynolds Alex Reynolds • written by jye • jye

Do you mean you just want to search the string "GATCGATGC" across the genome fasta and get the coordinates ?

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written by GouthamAtla GouthamAtla

This is probably the best thing to do, because if a read starts with "ATCGATGC" (no G at the beginning) then it is probably still relevant information to you. It is therefore probably best to find the genomic regions for GATCGATGC, then count the reads that fall anywhere over those regions, rather than the much more expensive computation of GATCGATGC in reads (with mismatches, etc)

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written by John John

Yes. That's what I want to do

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written by jye • jye

2 answers

EMBOSS has the tool fuzznuc, you can execute it in Galaxy and then convert the output to the desired format. Fuzznuc has several output formats, such as table or gff, one of them should work for you.

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written by Asaf Asaf

good to know. Have not come across this before.

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written by GouthamAtla GouthamAtla

That's a great tool. Solved my problem! Thank you!

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written by jye • jye

UCSC BLAT is not ideal for short sequences, but a command-line version of BLAT could be used locally with a small tile size and options -minMatch and -minIdentity to export a PSL file, and from there, a conversion script like psl2bed can be used to get a BED file for downstream set operations.

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written by Alex Reynolds Alex Reynolds

Thank you. Good to know.

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written by jye • jye

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