About Chromosome Y

[guanghaoli]

I have run TItanCNA for many times and found that the result doesn't contain Y chromosome. The manual of TItanCNA has said that TITAN converts chromosome X-> 23 and Y->24. Why do the results of Y chromosome disappear?
Here is my log file:
Parsing: fixedStep chrom=1 start=1 step=1000 span=1000
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Parsing: fixedStep chrom=3 start=1 step=1000 span=1000
Parsing: fixedStep chrom=4 start=1 step=1000 span=1000
Parsing: fixedStep chrom=5 start=1 step=1000 span=1000
Parsing: fixedStep chrom=6 start=1 step=1000 span=1000
Parsing: fixedStep chrom=7 start=1 step=1000 span=1000
Parsing: fixedStep chrom=8 start=1 step=1000 span=1000
Parsing: fixedStep chrom=9 start=1 step=1000 span=1000
Parsing: fixedStep chrom=10 start=1 step=1000 span=1000
Parsing: fixedStep chrom=11 start=1 step=1000 span=1000
Parsing: fixedStep chrom=12 start=1 step=1000 span=1000
Parsing: fixedStep chrom=13 start=1 step=1000 span=1000
Parsing: fixedStep chrom=14 start=1 step=1000 span=1000
Parsing: fixedStep chrom=15 start=1 step=1000 span=1000
Parsing: fixedStep chrom=16 start=1 step=1000 span=1000
Parsing: fixedStep chrom=17 start=1 step=1000 span=1000
Parsing: fixedStep chrom=18 start=1 step=1000 span=1000
Parsing: fixedStep chrom=19 start=1 step=1000 span=1000
Parsing: fixedStep chrom=20 start=1 step=1000 span=1000
Parsing: fixedStep chrom=21 start=1 step=1000 span=1000
Parsing: fixedStep chrom=22 start=1 step=1000 span=1000
Parsing: fixedStep chrom=X start=1 step=1000 span=1000
Parsing: fixedStep chrom=Y start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Correcting Tumour
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Correcting Normal
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Normalizing Tumour by Normal
Warning messages:
1: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
EOF within quoted string
2: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
EOF within quoted string
3: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
EOF within quoted string
4: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
EOF within quoted string
Removed Chrs:
Warning message:
In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
EOF within quoted string
titan: Running HMM...
fwdBack: Iteration 1 chr: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

You can see that the input file have 24 chromosomes. While the program iterates in HMM, there are only 23 chromosomes. How does it happen?

[gavinha]

Hi @guanghaoli

By default, the script excludes chrY. If you are using the snakemake workflow, you can modify this in the config.yaml file. Otherwise, you may have to adjust your arguments for the R scripts.

Best,
Gavin

[guanghaoli]

Thank you Gavin @gavinha. I'll try to adjust the arguments.

Best,
Guanghao