Mapping annotation to genome positions

[EulnayM]

Hi all,

I am looking for a faster method to map annotation I obtained from RAST to a range of target genome positions.

The method I am currently using is by filtering the start and end position in the excel file to my target range (for example if I am finding annotated CDS that locates between 49050 and 54500 bp, I filter the genome location of the annotation file to "larger or equal to 49050" and "less than or equal to 54500" and copy the related result from there.

This method is extremely time-consuming and now I have a set of data with about 500 ranges so I am looking for suggestions on any method that I can use to speed up this process? I know very limited awk and R but is familiar with usage of Linux OS.

Thank you in advance for any help

[SylvainL]

Hi,
the easiest (and fastest) would be to go either using the packages Rsamtools (including GRanges) and rtracklayer on R, or bedtools...

[WhatsOEver]

Although I agree with SylvainL that R should be faster than awk in this case you should not underestimate the power of linux tools for tasks like this. A simple script using awk how this could look like is the following (it expects bed format in its current version):

#!/bin/sh

#example call: thisScriptName.sh coordinatesFile dataFile outputFile

#$1 (coordinatesFile) to be the file with your coordinates you want to select for
#$2 (dataFile) to contain your data
#$3 (outputFile) is the file you want to save your results to

IFS='
' #use line break as end of line separator
#loop through lines of your coordinatesFile and for each line look in your data file
for line in $(cat $1)
do
lowLimit=$(echo $line | awk -F'\t' '{print $2}')
highLimit=$(echo $line | awk -F'\t' '{print $3}')
awk '{OFS="\t"; if(($2>'$lowLimit' && $2<'$highLimit') || ($3>'$lowLimit' && $3<'$highLimit')) print $0}' $2 >> $3
done

[AlexReynolds]

BEDOPS offers bedmap, for mapping features from one BED file to another. It is fast and efficient, and supported on Linux. Operations are offered that work with numerical and categorical features.

More information is available here:

http://bedops.readthedocs.org/en/latest/content/reference/statistics/bedmap.html

Be careful when converting Excel output to BED, in that Microsoft adds special endline characters that interfere with the functionality of bedmap and other Unix tools. The "dos2unix" application is useful here for cleaning Excel-sourced text files:

http://bedops.readthedocs.org/en/latest/content/reference/statistics/bedmap.html#endlines