Format of exons bed file

[chowbina]

Hello,

What is the format of the exons bed file as input to ichorCNA?

Thank you, Sudhir

[jurhoades]

Hi Sudhir,

The format should be BED format. ichorCNA expects a tab delimited file where the first column is the chromosome, the second is the start position, and the third is the end position. It also currently requires column headers, although it doesn't care about the exact naming. An example could look like this:

chr    start    stop
1      100      200
1      250      300
2      101      400
etc...

It should be ok if there are additional columns but ichorCNA will only look at the first three. Hope this helps!

[chowbina]

Hi Justin,

Thank you for the reply. This format is working and the command is not providing any error.

However, I do not see metrics specific to those exon regions that I have provided?

Here is the command that I used:

Rscript runIchorCNA.R --id tumor_sample --WIG $TUMOR_WIG --NORMWIG $NORMAL_WIG --ploidy "c(2,3)" --normal "c(0.5,0.6,0.7,0.8,0.9)" --maxCN 10 --gcWig $GC_WIG --mapWig $MAP_WIG --centromere $CENT_WIG --includeHOMD False --chrs "c(1:22)" --chrTrain "c(1:22)" --estimateNormal False --estimatePloidy False --estimateScPrevalence False --scStates "c(1,3)" --outDir $OUTDIR --exons.bed $EXONS_BED

tumor_sample.correctedDepth.txt still shows at intervals of 999999

chr	start	end	log2_TNratio_corrected
1	2000001	3000000	NA
1	8000001	9000000	0.154257665720098
1	9000001	10000000	-0.0836845239367425

Thank you, Sudhir

[gavinha]

Hi Sudhir,

The exon/targeted interval file is used to select (via overlap) the bins from the WIG files. The normalization approach used by ichorCNA requires equal sized, non-overlapping bins; therefore, it will not return results for the exon intervals.
You can try to use small bin sizes (e.g. 25kb or 50kb) to try to increase resolution of the exons.

Best, Gavin

[chowbina]

Hello, I ran the readcounter and ichorCNA command with 500kb intervals, used 500kb Gc and map file, tried bed file with window size of 50kb and 500kb; but could not get it to work. I get the following error:

Correcting for GC bias...
Error in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  span is too small
Calls: loadReadCountsFromWig -> correctReadCounts -> loess -> simpleLoess
In addition: Warning message:
In .replace_seqlevels_style(x_seqlevels, value) :
  found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one
Execution halted

[ilykos]

What is the main idea behind --exons.bed parameter? Is it used to make to narrow the analysis to exons in WES data? Or can it be used in WGS too?