No I currently do not, to save time. I will try it with the GEM file though. I'll let you know how it goes!
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If it looks like:
Code:hs1 1631000 1731000 3.953692 hs1 1731000 1831000 3.953692 hs1 1831000 1931000 3.953692 hs1 1931000 2031000 3.953692
Code:<plot> show = yes type = scatter file = yourFile.CNP.circos.txt glyph = rectangle glyph_size = 4 fill_color = dgrey stroke_color = dgrey stroke_thickness = 1 min = 0 max = 6 #r0 = 0.7r #r1 = 0.975r r0 = 0.76r r1 = 0.975r background = no background_color = vvlgrey background_stroke_color = black background_stroke_thickness = 1 axis = yes axis_color = lgrey axis_thickness = 1 axis_spacing = 1 <rules> <rule> importance = 100 condition = var(value) >= 6 value=6 glyph = rectangle glyph_size = 4 fill_color = red stroke_color = red stroke_thickness = 1 </rule> <rule> importance = 100 condition = var(value) > 2.5 && var(value) < 6 glyph = rectangle glyph_size = 4 fill_color = orange stroke_color = orange stroke_thickness = 1 </rule> <rule> importance = 85 condition = var(value) < 1.5 glyph_size = 4 fill_color = blue stroke_color = blue stroke_thickness = 1 </rule> <rule> show=0 importance = 85 condition = var(value) < 0 color = blue </rule> </rules> </plot>
Last edited by valeu; 07-30-2014, 07:00 AM.
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Calling CNA and BAF for exome seq data without a control
Hi, I'm trying to use FREEC to call CNA and BAF in some exome seq samples, but haven't been able to make it work. The tool ran fine on the chr19 test data.
The problems I'm seeing are
- the tool runs but doesn't generate any of the output files except mpileup.txt_sample.cpn
It exits with the error message:
..There is no control sample!!!
You have to use a matching control sample to get adequite results since GC-bias is not the only bias in targeted sequencing
- even the .cpn file doesn't seem right because it tries to call copy number outside the target regions I provided via the TruSeq_exome_targeted_regions.hg19.bed
and not surprisingly calls them all as 0 copy number.
I'm running the tool on a pileup generated using samtools v.0.1.12. I'm using the following config file:
[general]
chrLenFile=hg19.len
window = 3000
step = 1000
ploidy = 2
#breakPointThreshold = -.001
#GCcontentProfile = GC_profile.cnp
intercept=1
minMappabilityPerWindow = 0.7
outputDir = .
sex=XY
breakPointType=4
#degree=3
#coefficientOfVariation = 0.05
#gemMappabilityFile = /hg19/out76_hg19.gem
chrFiles = FREEC_Linux64/chromosomes/
[sample]
mateFile=mpileup.txt
#mateCopyNumberFile=mpileup.txt_sample.cpn
inputFormat = pileup
mateOrientation = FR
[control]
[BAF]
SNPfile = hg19_snp131.SingleDiNucl.1based.txt
minimalCoveragePerPosition = 5
[target]
captureRegions=TruSeq_exome_targeted_regions.hg19.bed
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Hi!
I think I should right a script to create a .WIG file from _ratio.txt (http://www.broadinstitute.org/igv/WIG)
If you code in perl, you could do it yourself and share the script. Otherwise, I will do it when I have time
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Version 5.7 of Control-FREEC can now create BedGraph tracks on demand. Just set
Code:[general] BedGraphOutput=TRUE
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Hi,
I have not foreseen an option to create a GC-content profile outside of FREEC. But you could make a trick: something like providing a read file with 10 reads and setting a window size.
I will think about adding a separate function to calculate this profile.
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Hi,
so now you can generate a GC-content profile independently from FREEC:
http://bioinfo-out.curie.fr/projects...orial.html#GCP
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a unusual problem in FREEC
I meet an unusual problem when I run FREEC. If I provide a mateCopyNumberFile, and then qsub, it will run sucessfully, but in fact I normally don't have mateCopyNumberFile, but if I don't provide it, it can't run, the error message is:
sh:samtools:command not found
Error: FREEC was not able to extract reads from /database/chenxi/task/cancerProgram/pipline/bwa/BPMICS4/sortedbam/PD1W_XXL_BPMICS4_NoIndex_modified.bam
Check your parameters: inputFormat and matesOrientation
Use "matesOrientation=0" if you have single end reads
Check the list of possible input formats at http://bioinfo-out.curie.fr/projects...al.html#CONFIG
I can't figure out what happens here. My parameters are absolutely correct, and I have samtools in my working directory and environmental PATH.
Can anyone give me some helps? I am not able to run FREEC because of this.
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I think I know what happens. When you provide mateCopyNumberFile, FREEC does not try to read your .BAM file. When there is no mateCopyNumberFile available FREEC tries to read your file by calling "samtools" in the command line. And it seems that "samtools" does not point to anything.
I would suggest two solutions:
- in the bash script that you qsub, add something like
Code:
export PATH=$PATH:/pathToSamtools #check whether samtools exists samtools 2>samtools.usage.txt #run FREEC freec -conf myCofig.txt
- transform you .BAM file to .SAM. Then, FREEC will not need samtools.
If you prefer, you can write to me directly to [email protected]
Comment
- in the bash script that you qsub, add something like
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