Question: bedGraphToBigWig error - end coordinate bigger than chr
0
gravatar for varsha619
11 months ago by
varsha61970
varsha61970 wrote:

Does anyone know a way to fix the bedGraphToBigWig error - end coordinate bigger than chr? My input is a bedGraph generated using MACS2. This link suggests using bedClip - https://groups.google.com/forum/embed/#!topic/macs-announcement/gXdf115Xy5Q. But I would like to know if there is a command line option to fix it. Thank you for your help.

bedgraphtobigwig macs2 • 605 views
ADD COMMENTlink modified 11 months ago by Alex Reynolds24k • written 11 months ago by varsha61970

Fixed it with bedClip, thank you for your help!

ADD REPLYlink written 11 months ago by varsha61970
1
gravatar for genecats.ucsc
11 months ago by
genecats.ucsc500
genecats.ucsc500 wrote:

bedClip is a command line program to do this:

bedClip input.bed http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes output.bed

You can download bedClip from the directory appropriate to your operating system within our directory of utilities.

If you have questions about running bedClip, feel free to send a question to one of our mailing lists:

  • genome@soe.ucsc.edu for general questions
  • genome-mirror@soe.ucsc.edu for questions involving mirrors or gbibs
  • genome-www@soe.ucsc.edu for questions involving private data

ChrisL from the UCSC Genome Browser

ADD COMMENTlink written 11 months ago by genecats.ucsc500
0
gravatar for Pierre Lindenbaum
11 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum108k wrote:

generate a awk script that will clip your bed records:

mysql --user=genome -N --host=genome-mysql.cse.ucsc.edu -A -D hg19  -e 'select chrom,size from chromInfo '  |\
awk '{printf("($1==\"%s\") {L=%d;B=int($2);E=int($3);B=(B>=L?L:B);E=(E>=L?L:E);printf(\"%s\\t%%d\\t%%d\\n\",B,E);next;}\n",$1,$2,$1);}' > script.awk



$ head  script.awk
($1=="chr1") {L=249250621;B=int($2);E=int($3);B=(B>=L?L:B);E=(E>=L?L:E);printf("chr1\t%d\t%d\n",B,E);next;}
($1=="chr2") {L=243199373;B=int($2);E=int($3);B=(B>=L?L:B);E=(E>=L?L:E);printf("chr2\t%d\t%d\n",B,E);next;}
($1=="chr3") {L=198022430;B=int($2);E=int($3);B=(B>=L?L:B);E=(E>=L?L:E);printf("chr3\t%d\t%d\n",B,E);next;}
($1=="chr4") {L=191154276;B=int($2);E=int($3);B=(B>=L?L:B);E=(E>=L?L:E);printf("chr4\t%d\t%d\n",B,E);next;}
($1=="chr5") {L=180915260;B=int($2);E=int($3);B=(B>=L?L:B);E=(E>=L?L:E);printf("chr5\t%d\t%d\n",B,E);next;}
($1=="chr6") {L=171115067;B=int($2);E=int($3);B=(B>=L?L:B);E=(E>=L?L:E);printf("chr6\t%d\t%d\n",B,E);next;}
($1=="chr7") {L=159138663;B=int($2);E=int($3);B=(B>=L?L:B);E=(E>=L?L:E);printf("chr7\t%d\t%d\n",B,E);next;}
($1=="chrX") {L=155270560;B=int($2);E=int($3);B=(B>=L?L:B);E=(E>=L?L:E);printf("chrX\t%d\t%d\n",B,E);next;}
($1=="chr8") {L=146364022;B=int($2);E=int($3);B=(B>=L?L:B);E=(E>=L?L:E);printf("chr8\t%d\t%d\n",B,E);next;}
($1=="chr9") {L=141213431;B=int($2);E=int($3);B=(B>=L?L:B);E=(E>=L?L:E);printf("chr9\t%d\t%d\n",B,E);next;}

then use this awk script :

awk -f  script.awk input.bed
ADD COMMENTlink written 11 months ago by Pierre Lindenbaum108k
0
gravatar for Alex Reynolds
11 months ago by
Alex Reynolds24k
Seattle, WA USA
Alex Reynolds24k wrote:

To solve this problem more generically, make a BED file and use that as a mask with BEDOPS bedops --element-of:

$ fetchChromSizes hg38 | awk '{ print $1"\t0\t"$2; }" | sort-bed - > hg38.bed
$ bedops --element-of 1 in.bedGraph hg38.bed > masked.in.bedGraph

Then convert the masked bedGraph file to Wiggle format.

But mainly I'd be concerned about having signal get generated in regions that don't or shouldn't exist. That might point to a potential data problem or code smell, somewhere.

ADD COMMENTlink modified 11 months ago • written 11 months ago by Alex Reynolds24k
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