[yuhao]

I am very appreciated for your patient help! I have some other questions to see if I can get your help:

The output intervals have some overlaps, e.x., 58000, 8387999, 3 gain, 8386000, 9404999 5 gain , so 8386000 < 8387999, how could this thing happen?

What does control database mean here?Normally we just have a test genome and a reference genome.

As far as I know, there are typically two different methods to call CNV, segmentation based, and hidden markov model, I am wondering if FREEC is based on segmentation based method?

How do we determine the window size and steps parameters? Which parameters can affect the accuracy of the result, that's very crucial for the result so I care much about this?

Finally, aside from FREEC, can you recommend some other softwares which had been widely used for CNV detection in the world (because I have many choices but I don't know which ones are best among all). I also tried CNVnator, but the result seems very different from FREEC.

I appreciate your help!

[valeu]

"ratio" is actually "normalized read count". Values around 1 correspond to the main ploidy of the sample.

If you use a control sample and you set degree=1, then "ratio" is simply the ratio of read count in the sample and read count in the control.

[yuhao]

May I ask a question, what does the "ratio" mean in FREEC? Thanks!

[yuhao]

Thank you for your help! I meet another question: I want to plot the graph using makeGraph.R , when I run, it shows:

null device
1
Error in if (type.convert(args[6])) { :
missing value where TRUE/FALSE needed
Execution halted

Can you give me some help ? Thank you !

[valeu]

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:

1. in the bash script that you qsub, add something like

   export PATH=$PATH:/pathToSamtools
   #check whether samtools exists
   samtools 2>samtools.usage.txt
   #run FREEC
   freec -conf myCofig.txt

1. transform you .BAM file to .SAM. Then, FREEC will not need samtools.

If you prefer, you can write to me directly to [email protected]

[yuhao]

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.

[valeu]

Hi,

so now you can generate a GC-content profile independently from FREEC:

http://bioinfo-out.curie.fr/projects/freec/tutorial.html#GCP

[valeu]

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.

[monkeychild]

Hi

I am (slowly) trying to integrate Control-FREEC into a pipeline, and I was wondering if there's a way to generate a GC-content profile outside of running the whole thing once. Like maybe one of the already existing scripts could be called outside of freec first?

[valeu]

Version 5.7 of Control-FREEC can now create BedGraph tracks on demand. Just set

[general]
BedGraphOutput=TRUE

This format is supported by the UCSC genome browser as well as IGV (http://www.broadinstitute.org/software/igv/bedgraph)

[bwt4383]

Thanks for your reply! It would be very helpful if you could implement a script for .WIG file creation!
:-)

[valeu]

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

[bwt4383]

Display of CNV-data in IGV

Hi, I am struggling with displaying CNV data generated with freec in IGV. Can somebody give me some advice how to display CNVs in an inutitive way?

Thanks!

[bw.]

That would really useful!
My backup was to use per-exon mean target coverage generated by Picard HS Metrics, with some added correction for %GC, but I'd rather use your tool.
Thanks,
-Ben

[valeu]

Hi, at this moment there is no option to run FREEC on exome-seq data without control sample. But since you are the second person who wants to do it, I will probably add this option soon.