*rds, mappability and gc wig files for more bin sizes

[andreykoch]

Hi Gavin,

I appreciate you adding GC and mappability 50Kb wig files. I was wondering if you could generate them for Hg19 as well and add HD_ULP_***_median_normAutosome_median.rds for 50Kb?

Thank you, Andrey

[gavinha]

Hi @andreykoch

I have included GC and map wig files for 50kb and 10kb. For the normal panel, unfortunately, the ultra-low coverage (0.1x) is not sufficient to generate a panel for 50kb. I am not sure the read coverage of your data but if it is also ~0.1x I would not recommend using 50kb. If you are using much deeper coverage, then using a matched normal would be a much better suited for normalization.

Hope this helps, Gavin

[andreykoch]

Hi Gavin,

Thanks for your input. The data I have has x0.4 coverage, so hopefully it should be sufficient to generate PoN with 50Kb bins.

On the other hand, I'm experiencing hickups with generating PoN with the error message similar to the issue24.

I have previously generated 4 normal wig files using

$readCounter --window 50000 --quality 20 --chromosome "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY" $normal_sample.bam > $normal_sample.wig

And they look OK, e.g. fixedStep chrom=chr1 start=1 step=50000 span=50000 5 47 31

The actual command line for the PoN generation looks like this:

Rscript /rdseqdata/bin/ichorCNA-master/scripts/createPanelOfNormals.R
--filelist /rndhome/akoch/SamBam_file_example/TMP/ref/wigPoNfiles.txt
--gcWig /rdseqdata/bin/ichorCNA-master/inst/extdata/gc_hg19_50kb.wig
--mapWig /rdseqdata/bin/ichorCNA-master/inst/extdata/map_hg19_50kb.wig
--centromere /rdseqdata/bin/ichorCNA-master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt
--outfile /rdseqdata/bin/ichorCNA-master/inst/extdata/PoN_hg19_50Kb_median_normAutosome_median.rds

And the output before blowup looks like this:

Loading normal file:/rndhome/akoch/SamBam_file_example/TMP/ref/1801100551-NIK-3-26_TCATCTCC_L003_R1_export.wig Slurping: /rndhome/akoch/SamBam_file_example/TMP/ref/1801100551-NIK-3-26_TCATCTCC_L003_R1_export.wig Parsing: fixedStep chrom=chr1 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr2 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr3 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr4 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr5 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr6 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr7 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr8 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr9 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr10 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr11 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr12 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr13 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr14 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr15 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr16 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr17 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr18 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr19 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr20 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr21 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chr22 start=1 step=50000 span=50000 Parsing: fixedStep chrom=chrX start=1 step=50000 span=50000 Parsing: fixedStep chrom=chrY start=1 step=50000 span=50000 Sorting by decreasing chromosome size Reading GC and mappability files Slurping: /rdseqdata/bin/ichorCNA-master/inst/extdata/gc_hg19_50kb.wig Parsing:

fixedStep chrom=1 start=1 step=50000 span=50000 Error in seq.default(from = as.integer(tokens[2]), by = as.integer(tokens[3]), : 'from' must be a finite number Calls: wigToRangedData -> seq -> seq.default Execution halted

I would appreciate any hints on what is going on.

Andrey

[haojam]

Hi Gavin, Could you please generate GC and map wig files for 200bins and share the same (gc_hg38_200kb.wig & map_hg38_200kb.wig) for an internal research purpose.

Regards, Rocky