Support for multiple patterns in nucBed

[obot]

Hello all,
The nucBed tool is great for generating statistics about a bunch of
genome locations, thank you for creating it. I am interested in
analyzing dinculeotide content (eg counts of the sixteen dinucleotide
combinations of AT vs TA vs AC vs CA, etc) in transcripts. Currently,
nucBed supports a single user-specified pattern to add to the suite of
other features it surveys, and to analyze these, I would need to run
nucBed 16 times, once for each combination. Is it possible to add
support for multiple patterns in nucBed?
Warmest,
Olga

[Aaron Quinlan]

Hi Olga,

It is certainly possible to support multiple patterns, but I am not certain that this is a better approach than running a distinct command for each pattern. Is the primary bottleneck for you the computational time or the act of combining the results?

Best,
Aaron

[Aaron Quinlan]

Hi Husen,

This sort of fuzzy matching is beyond the current abilities in bedtools.  Perhaps you could use one of the utilities in the EMBOSS suite?

- Aaron

quinlanlab.org

On Jun 3, 2013, at 11:53 AM, Husen Muhammad <husens...@gmail.com> wrote:

Hi,

Thank you for providing BedTools such a great all-in-one tool. 

I want to use nucBed to find occurrences of a given pattern in a bed file. According to my testing, -pattern does not accept regular expressions to search for variances of a sequence. It would be great and efficient to e able to search for variances of a pattern in one run instead of testing all the combinations iteratively. 

Example:

cat test.fa:

>seq1

GCAGCAGAGGTCAGCAAG

cat test.bed:

chr1 2 9

command: nucBed -fi test.fa -bed test.bed -pattern CANCANNC

I want seq1 be reported as a matched sequence for the given pattern.

Best wishes,

Husen

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