All CpGs methylated?
mjmc...@gmail.com
I'm working on a project in the Wang lab, and I'm having some problems using methylCRF. When I try to view the *_methylCRF.bed file on the UCSC genome browser, it shows that every CpG is methylated in the genome across all my samples. Here is the err file associated with one of my attempts:
Thu Sep 5 08:52:34 2013 format MeDIP_TW210_FibNSd14.fastq.gz.bam.crfdip and TW199_MRE.bed.nocontig
-rw-rw-r-- 1 mmccoy mmccoy 837831812 Sep 5 2013 cpg_MeDIP_TW210_FibNSd14.fastq.gz.bam.crfdip_read.bed
p75:7021288 P75cnt:+
-rw-rw-r-- 1 mmccoy mmccoy 0 Sep 5 08:38 MeDIP_TW210_FibNSd14.fastq.gz.bam.crfdip
-rw-rw-r-- 1 mmccoy mmccoy 0 Sep 5 08:52 MeDIP_TW210_FibNSd14.fastq.gz.bam.crfdip.norm.bed
-rw-rw-r-- 1 mmccoy mmccoy 3744020 Sep 5 08:52 TW199_MRE.bed.nocontig
Thu Sep 5 08:55:04 2013 make avg windows for MeDIP_TW210_FibNSd14.fastq.gz.bam.crfdip and TW199_MRE.bed.nocontig
0
10
100
1000
10000
0
10
100
1000
10000
28085155 56170310 493965481 FibNSd14_DIP_d0.cnt
28085155 56170310 494087967 FibNSd14_MRE_d0.cnt
28085155 56170310 493965481 FibNSd14_DIP_d10.cnt
28085155 56170310 494267987 FibNSd14_MRE_d10.cnt
28085155 56170310 493965481 FibNSd14_DIP_d100.cnt
28085155 56170310 495287418 FibNSd14_MRE_d100.cnt
28085155 56170310 493965481 FibNSd14_DIP_d1000.cnt
28085155 56170310 499505583 FibNSd14_MRE_d1000.cnt
28085155 56170310 493965481 FibNSd14_DIP_d10000.cnt
28085155 56170310 512389863 FibNSd14_MRE_d10000.cnt
FibNSd14_DIPMRE.cnt column numbers
11
Thu Sep 5 09:13:55 2013 making DIPMRE.cnt for MeDIP_TW210_FibNSd14.fastq.gz.bam.crfdip and TW199_MRE.bed.nocontig
FibNSd14_DIPMRE.cnt column numbers
11
Thu Sep 5 09:14:57 2013 make table
FibNSd14_cpgi.tbl
17
0
FibNSd14_cpgi_1kshore.tbl
17
0
FibNSd14_cpgi_2kshore.tbl
17
0
FibNSd14_distal_promoter.tbl
17
0
FibNSd14_proximal_promoter.tbl
17
0
FibNSd14_core_promoter.tbl
17
0
FibNSd14_utr5.tbl
17
0
FibNSd14_exon.tbl
17
0
FibNSd14_intron.tbl
17
0
FibNSd14_utr3.tbl
17
0
FibNSd14_gene_body.tbl
17
0
FibNSd14_rmsk_lowsimple.tbl
17
0
FibNSd14_rmsk_RNA.tbl
17
0
FibNSd14_rmsk_LTR.tbl
17
0
FibNSd14_rmsk_DNA.tbl
17
0
FibNSd14_rmsk_SINE.tbl
17
0
FibNSd14_rmsk_LINE.tbl
17
0
FibNSd14_rmsk_other.tbl
17
0
FibNSd14_notAnno.tbl
17
0
Thu Sep 5 10:30:52 2013 predict
predict: [cpgi] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/cpgi.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 10413040 Sep 5 2013 FibNSd14_cpgi.tbl_h1es_mdl.out
predict: [cpgi_1kshore] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/cpgi_1kshore.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 6965273 Sep 5 2013 FibNSd14_cpgi_1kshore.tbl_h1es_mdl.out
predict: [cpgi_2kshore] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/cpgi_2kshore.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 11396787 Sep 5 2013 FibNSd14_cpgi_2kshore.tbl_h1es_mdl.out
predict: [distal_promoter] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/distal_promoter.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 6934583 Sep 5 2013 FibNSd14_distal_promoter.tbl_h1es_mdl.out
predict: [proximal_promoter] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/proximal_promoter.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 1965235 Sep 5 2013 FibNSd14_proximal_promoter.tbl_h1es_mdl.out
predict: [core_promoter] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/core_promoter.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 700040 Sep 5 2013 FibNSd14_core_promoter.tbl_h1es_mdl.out
predict: [utr5] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/utr5.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 1726720 Sep 5 2013 FibNSd14_utr5.tbl_h1es_mdl.out
predict: [exon] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/exon.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 9237975 Sep 5 2013 FibNSd14_exon.tbl_h1es_mdl.out
predict: [intron] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/intron.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 59133096 Sep 5 2013 FibNSd14_intron.tbl_h1es_mdl.out
predict: [utr3] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/utr3.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 1556104 Sep 5 2013 FibNSd14_utr3.tbl_h1es_mdl.out
predict: [gene_body] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/gene_body.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 67464371 Sep 5 2013 FibNSd14_gene_body.tbl_h1es_mdl.out
predict: [rmsk_lowsimple] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/rmsk_lowsimple.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 2058863 Sep 5 2013 FibNSd14_rmsk_lowsimple.tbl_h1es_mdl.out
predict: [rmsk_RNA] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/rmsk_RNA.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 89015 Sep 5 2013 FibNSd14_rmsk_RNA.tbl_h1es_mdl.out
predict: [rmsk_LTR] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/rmsk_LTR.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 10531615 Sep 5 2013 FibNSd14_rmsk_LTR.tbl_h1es_mdl.out
predict: [rmsk_DNA] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/rmsk_DNA.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 3239180 Sep 5 2013 FibNSd14_rmsk_DNA.tbl_h1es_mdl.out
predict: [rmsk_SINE] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/rmsk_SINE.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 39671303 Sep 5 2013 FibNSd14_rmsk_SINE.tbl_h1es_mdl.out
predict: [rmsk_LINE] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/rmsk_LINE.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 17272300 Sep 5 2013 FibNSd14_rmsk_LINE.tbl_h1es_mdl.out
predict: [rmsk_other] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/rmsk_other.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 1365510 Sep 5 2013 FibNSd14_rmsk_other.tbl_h1es_mdl.out
predict: [notAnno] [/expr/mmccoy/neurons/methylCRF/h1es_mdl/notAnno.mdl]
-rw-rw-r-- 1 mmccoy mmccoy 24454470 Sep 5 2013 FibNSd14_notAnno.tbl_h1es_mdl.out
Thu Sep 5 12:31:01 2013 making ensemble prediction
Thu Sep 5 12:52:40 2013 fin
What's going on? Please let me know if I can provide any other information.
Thanks,
Matt
michael
Could you please show me the top 10 lines or so of the DIP and MRE bed files? You can use: http://pastebin.com/
thx!
michael
michael
It does sound right if the numbers range from 0-1. On the browser you
can click on a track to configure it -check to see that the range is set
to 0-1. If it still doesn't change, how did you load the data onto the
browsre?
michael
On 09/06/2013 02:22 PM, Matt McCoy wrote:
> Hi Michael,
>
> Actually, I think it might only be a problem with the way I am viewing
> the final <File_name>_mCRF.bed file on the UCSC genome browser. Here's
> the first few lines of the file:
>
> 1.
> track name='<File_name>_mCRF'
> 2.
> chr1 10468 10470 chr1.1 0.98
> 3.
> chr1 10470 10472 chr1.2 0.98
> 4.
> chr1 10483 10485 chr1.3 0.98
> 5.
> chr1 10488 10490 chr1.4 0.98
> 6.
> chr1 10492 10494 chr1.5 0.98
> 7.
> chr1 10496 10498 chr1.6 0.98
> 8.
> chr1 10524 10526 chr1.7 0.98
>
>
> Does this look okay to you?
>
> The number in column 5 ranges from 0-1. If it is only a viewing problem,
> do you know how to get the UCSC genome browser to cooperate with me?
>
> Thanks,
> Matt
>
>
> On Fri, Sep 6, 2013 at 12:21 PM, Matt McCoy <mjmc...@gmail.com
> <mailto:mjmc...@gmail.com>> wrote:
>
> Hi Michael,
>
> Thanks for the quick response!
>
> Here are the first 10 lines of one of my MeDIP.crfdip files:
>
> 1.
> chr1 10000 10166 . 1 +
> 2.
> chr1 10000 10353 . 1 +
> 3.
> chr1 10000 10139 . 1 +
> 4.
> chr1 10000 10136 . 1 +
> 5.
> chr1 10000 10133 . 1 +
> 6.
> chr1 10000 10225 . 1 +
> 7.
> chr1 10000 10132 . 1 +
> 8.
> chr1 10001 10280 . 1 +
> 9.
> chr1 10001 10170 . 1 +
> 10.
> chr1 10001 10285 . 1 +
>
>
> Here is the MeDIP.fastq.gz.extended.bed file that I used to generate
> the MeDIP.crfdip file:
>
> 1.
> chr1 10000 10166
> CCCTTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACAGAT
> 29 +
> 2.
> chr1 10000 10353
> TAACACTAACCCTAACCCTAACCCTAACCCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCAACCCCAAC
> 29 +
> 3.
> chr1 10000 10139
> AACCCCTAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAA
> 12 +
> 4.
> chr1 10000 10136
> AACCCTAACCCTAACCCTACCCAACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACCCAACCCTAA
> 29 +
> 5.
> chr1 10000 10133
> CCTCACCCTCACCCTCACCCTCACCCTCACCCTCACCCTCACCCTCACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACCCTAACCCT
> 29 +
> 6.
> chr1 10000 10225
> TAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTCTAACCCTAC
> 10 +
> 7.
> chr1 10000 10132
> CCTAACCCTAACCCTAACCCTACCCCTAACCCAAACCCTAACCCTAACCCAAACCCTAACCCAAACCCAACCCCAACCCCAAACCCTACCCCTACCCTAAC
> 29 +
> 8.
> chr1 10001 10280
> AACCCTAACCCGAACCCGAACCCTAACCCTAACCCGAACCCGAACCCTAACCCGAACCCGAACCCCTAACCCTAACCCGAACCCTAACCCTAACCCTAACC
> 29 +
> 9.
> chr1 10001 10170
> AACCCTAACCCTAACCTTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCAACCCTAACCCTAACCC
> 29 +
> 10.
> chr1 10001 10285
> AACCCTAACCCTAACCCTACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTC
> 29 +
>
>
> And for my MRE.fastq.gz.bam file viewed with samtools:
>
> 1.
> :HWI-ST155_0743:4:2205:16956:33299#0 0 chr1 10000
> 0 42M ATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC
> bbbeeeeegggggffgghiegfghhfhfiiifgaghhdgegh XT:A:U NM:i:0
> XN:i:1 X0:i:1 X1:i:582 XM:i:0 XO:i:0 XG:i:0 MD:Z:42
> 2.
> :HWI-ST155_0743:3:1101:4062:43417#0 0 chr1 10001
> 0 42M TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
> ___eceeegg`ecgaghhdfdfgh_dghhhfhffhhgagff^ XT:A:R NM:i:0
> X0:i:575 XM:i:0 XO:i:0 XG:i:0 MD:Z:42
> 3.
> :HWI-ST155_0743:4:2213:12277:23726#0 0 chr1 10001
> 0 42M TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
> bbbeeeeegggggiiiiiiiiiiiiiiihfihhighdhhiic XT:A:R NM:i:0
> X0:i:575 XM:i:0 XO:i:0 XG:i:0 MD:Z:42
> 4.
> :HWI-ST155_0743:3:2215:1743:72688#0 0 chr1 10002
> 0 42M AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT
> bbbeeeeegggggiiiiihiiiihiiiiiihiiiiiiiiiih XT:A:R NM:i:0
> X0:i:567 XM:i:0 XO:i:0 XG:i:0 MD:Z:42
> 5.
> :HWI-ST155_0743:4:1116:14025:15954#0 16 chr1 10002
> 0 42M AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT
> hfihgefchihfgfihgff`hhgdediigeecggecc`eba_ XT:A:R NM:i:0
> X0:i:567 XM:i:0 XO:i:0 XG:i:0 MD:Z:42
> 6.
> :HWI-ST155_0743:4:1207:17600:51063#0 0 chr1 10002
> 0 42M AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT
> bbbeeeeeggggfighhfhhiiihiihgihhhehhe`fefhf XT:A:R NM:i:0
> X0:i:567 XM:i:0 XO:i:0 XG:i:0 MD:Z:42
> 7.
> :HWI-ST155_0743:3:2116:20818:7903#0 0 chr1 10003
> 0 42M ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
> bbbeeeeeggggfiiiihhiiiiiihiiiiiiiiiihiiiii XT:A:R NM:i:0
> X0:i:572 XM:i:0 XO:i:0 XG:i:0 MD:Z:42
> 8.
> :HWI-ST155_0743:4:2111:7587:48860#0 0 chr1 10003
> 0 42M ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
> bbbeeeeegggggiiihiiiiihihhfiiiiiihigfhhiii XT:A:R NM:i:0
> X0:i:572 XM:i:0 XO:i:0 XG:i:0 MD:Z:42
> 9.
> :HWI-ST155_0743:4:2316:13316:21190#0 0 chr1 10003
> 0 42M ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
> b_beeeeegggfgiiiihiiiiiiihiiiiiihihhhhghhi XT:A:R NM:i:0
> X0:i:572 XM:i:0 XO:i:0 XG:i:0 MD:Z:42
> 10.
> :HWI-ST155_0743:3:2205:3428:15263#0 16 chr1 10003
> 0 42M ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
> chgfefcihgdfdihgegdhhgdgeihgfgegggcdceea_a XT:A:R NM:i:0
> X0:i:572 XM:i:0 XO:i:0 XG:i:0 MD:Z:42
>
>
> My MRE.bed file that was generated from the MRE.fastq.gz.bam file
> with the script pasted after this:
>
> 1.
> chr10 100027739 100027741 . 47.7829
> 2.
> chr10 100027865 100027867 . 96.7680
> 3.
> chr10 100027867 100027869 . 75.4703
> 4.
> chr10 100027867 100027869 . 75.4703
> 5.
> chr10 100028496 100028498 . 75.4703
> 6.
> chr10 100028496 100028498 . 75.4703
> 7.
> chr10 100028498 100028500 . 96.7680
> 8.
> chr10 100101996 100101998 . 28.5124
> 9.
> chr10 100168372 100168374 . 28.5124
> 10.
> chr10 100227707 100227709 . 114.0495
>
>
> Also, here is part of the shell script I am using for this:
>
> 1.
> (samtools view $mre | sam2bed.pl <http://sam2bed.pl> -r -q 10 -
> )| MRE_norm.pl - MRE_5enz_4_6000.bed $mreAcc;
> 2.
> grep -vP 'random|Un|hap' ${mreAcc}_MRE.bed >
> ${mreAcc}_MRE.bed.nocontig;
> 3.
> methylCRF.pl h1es_mdl hg19_gdat ${dip}.crfdip
> ${mreAcc}_MRE.bed.nocontig MRE_5enz_4_6000_cpg.bin 750 $out >
> ${out}_mCRF.bed 2>err;
>
> Please let me know if I can provide any other information.
>
>
> Matt
>
> On Thu, Sep 5, 2013 at 3:30 PM, michael <ste...@cse.wustl.edu
> <mailto:ste...@cse.wustl.edu>> wrote:
>
> Hi Matt,
>
> Could you please show me the top 10 lines or so of the DIP and
> MRE bed files? You can use: http://pastebin.com/
>
> thx!
> michael
>
>
> On Thursday, September 5, 2013 2:03:23 PM UTC-5,
>
> Hello,
>
> I'm working on a project in the Wang lab, and I'm having
> some problems using methylCRF. When I try to view the
> *_methylCRF.bed file on the UCSC genome browser, it shows
> that every CpG is methylated in the genome across all my
> samples. Here is the err file associated with one of my
> attempts:
>
>
> Thu Sep 5 08:52:34 2013 format
> -rw-rw-r-- 1 mmccoy mmccoy 837831812 Sep 5 2013
> -rw-rw-r-- 1 mmccoy mmccoy 0 Sep 5 08:38
> TW199_MRE.bed.nocontig
> Thu Sep 5 08:55:04 2013 make avg windows for
> 0
> 10
> 100
> 1000
> 10000
> 0
> 10
> 100
> 1000
> 10000
> 28085155 56170310 493965481 FibNSd14_DIP_d0.cnt
> 28085155 56170310 494087967 FibNSd14_MRE_d0.cnt
> 28085155 56170310 493965481 FibNSd14_DIP_d10.cnt
> 28085155 56170310 494267987 FibNSd14_MRE_d10.cnt
> 28085155 56170310 493965481 FibNSd14_DIP_d100.cnt
> 28085155 56170310 495287418 FibNSd14_MRE_d100.cnt
> 28085155 56170310 493965481 FibNSd14_DIP_d1000.cnt
> 28085155 56170310 499505583 FibNSd14_MRE_d1000.cnt
> 28085155 56170310 493965481 FibNSd14_DIP_d10000.cnt
> 28085155 56170310 512389863 FibNSd14_MRE_d10000.cnt
> FibNSd14_DIPMRE.cnt column numbers
> 11
> Thu Sep 5 09:13:55 2013 making DIPMRE.cnt for
> FibNSd14_cpgi.tbl_h1es_mdl.out
> predict: [cpgi_1kshore]
> predict: [cpgi_2kshore]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/cpgi___2kshore.mdl]
> predict: [distal_promoter]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/distal___promoter.mdl]
> predict: [proximal_promoter]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/proximal___promoter.mdl]
> predict: [core_promoter]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/core___promoter.mdl]
> predict: [utr5]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/utr5.mdl]
> FibNSd14_utr5.tbl_h1es_mdl.out
> predict: [exon]
> FibNSd14_exon.tbl_h1es_mdl.out
> predict: [intron]
> predict: [utr3]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/utr3.mdl]
> FibNSd14_utr3.tbl_h1es_mdl.out
> predict: [gene_body]
> predict: [rmsk_lowsimple]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/rmsk___lowsimple.mdl]
> predict: [rmsk_RNA]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/rmsk_RNA.__mdl]
> predict: [rmsk_LTR]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/rmsk_LTR.__mdl]
> predict: [rmsk_DNA]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/rmsk_DNA.__mdl]
> predict: [rmsk_SINE]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/rmsk_SINE.__mdl]
> predict: [rmsk_LINE]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/rmsk_LINE.__mdl]
> predict: [rmsk_other]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/rmsk_other.__mdl]
> predict: [notAnno]
> [/expr/mmccoy/neurons/__methylCRF/h1es_mdl/notAnno.__mdl]
michael
Yeah, that's weird. I've never seen that. I usually use bed or bigWig.
Did you add a track description line or something that maybe specified
1000?
michael
On 09/06/2013 02:46 PM, Matt McCoy wrote:
> Hi Michael,
>
>
> When I click on the track, it only lets me set a score to cutoff at, and
> the range is stuck at 0-1000. I guess I could multiply all the scores by
> 100, and then set the score option at the top of my file with useScore=1...
>
> I uploaded this file via the custom tracks option.
>
> How do you normally visualize these files?
>
> Thanks,
> Matt
>
>
michael
No, I don't add any track lines. If you're using the remc browser,
maybe you can send me your hgsid and i can take a look?
michael
On 09/06/2013 03:30 PM, Matt McCoy wrote:
> Hi Michael,
>
> of the track.
>
> One last question: do you add any track lines to your files (e.g. to
> turn on grayscale, or the minimum/maximum scores)?
>
> I'm sure it just a matter of playing with the settings. I will update
> this later if I find a solution. Thanks for your help, anyway!
>
> Matt