Thanks for this,
I am using Terminal Version 2.2.2 (303) on Mac OSX Version 10.7.3
I tried the command that you sent: sed -e 's/^/chr/' inputFile.bed >
outputFile.bed and it did the first line but not the rest.
chr17 397142 397152 1
17 397152 397171 2
17 397171 397183 3
17 397183 397192 4
17 397192 397202 3
I get a similar result when I do:
awk '{print "chr"$1,$2,$3,$4}' inputFile.bed > outputFile.bed
awk '/^/{print "chr"$1,$2,$3,$4}' inputFile.bed > outputFile.bed
sed -i .bak 's/^/Chr/'inputFile.bed > outputFile.bed
sed -i '''s/^/Chr/' inputFile.bed > outputFile.bed
sed 's/^/^Chr/' inputFile.bed > outputFile.bed
and others…
How do I get it to do the other lines
genomeCoverageBed is part of the BedTools and it creates either a histogram,
BEDGRAPH, or a "per base" report of genome coverage. as you can see from here
http://code.google.com/p/bedtools/
The source files was a Bam file and corresponding .bai file.
Can UCSC generate a Coverage histogram is that possible?
Thank you.
-----------------------------------------------------
DeQuincy Prescott
Sen Res Tech to Professor Bhattacharya
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On 27 Feb 2012, at 17:49, Hiram Clawson wrote:
> Good Morning:
>
> Can you please clarify what the program 'genomeCoverageBed' is and what it is
> working on ?
> Did the source files you used with 'genomeCoverageBed' have the 'chr' prefix
> on the chromosome numbers ?
>
> You can simply change a file such as this with this sed command
> to place "chr" at the beginning of each line:
>
> sed -e 's/^/chr/' inputFile.bed > outputFile.bed
>
> You should be using chr instead of Chr if you are loading these tracks
> into the UCSC genome browser.
>
> --Hiram
>
> DeQuincy Prescott (UCL) wrote:
>> I managed to insert the header line however the genomeCoverageBed program
>> made each line without the "Chr" start
>> i.e.
>> 17 422997 422999 26
>> 17 422999 423001 27
>> 17 423001 423003 29
>> 17 423003 423010 28
>> 17 423010 423012 29
>> 17 423012 423013 32
>> 17 423013 423014 34
>> instead of Chr17 422997 422999 26
>> Chr17 422999 423001 27
>> Chr17 423001 423003 29
>> Chr17 423003 423010 28
>> Chr17 423010 423012 29
>> Chr17 423012 423013 32
>> Chr17 423013 423014 34
>> Is there a way to get "Chr" inserted at the beginning of each line or is
>> there a way to get UCSC to read the file without it?
>> Thanks
>> -----------------------------------------------------
>> DeQuincy Prescott
>> Sen Res Tech to Professor Bhattacharya
>
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