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Old 05-04-2018, 02:20 PM   #5
cursecatcher
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Location: Italy

Join Date: May 2018
Posts: 5
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Quote:
Originally Posted by Richard Finney View Post
NC_000016 is a name used for "chr16".
This the "official" name used at NCBI : https://www.ncbi.nlm.nih.gov/nuccore/NC_000016.10/

You have to convert the "NCBI name" to "chr" names (or vice versa).

There are many ways to rename fields. You can always brute force it using a custom simple program or script using your favorite programming language : bash, python, perl, C, etc.

Any easy way would be to reheader the bam file. Please see samtools documentation for this.
It works, thank you so much!!
I'm sorry for the triviality of the problem, but I'm not very practical with this stuff and the bedtools message wasn't very helpful.
Again, thank you!

Best regards
Nicola
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