Open SJRussell opened 4 years ago
Thanks for checking in, and sorry for the trouble.
Thanks for the response. For now:
Traceback (most recent call last): File "/home/stewart/anaconda3/envs/cnvkit/bin/cnvkit.py", line 8, in <module> from cnvlib import commands File "/home/stewart/cnvkit/cnvlib/__init__.py", line 4, in <module> from .cmdutil import read_cna as read File "/home/stewart/cnvkit/cnvlib/cmdutil.py", line 7, in <module> from .cnary import CopyNumArray as CNA File "/home/stewart/cnvkit/cnvlib/cnary.py", line 9, in <module> from . import core, descriptives, params, smoothing File "/home/stewart/cnvkit/cnvlib/smoothing.py", line 152 x, wing, *padded = check_inputs(x, width, False, weights) ^ SyntaxError: invalid syntax
By reinstalling with pip, the issues seem resolved. I also ran with -f counts
and it appears to give log2 values, suggesting that counts from STAR or HTSeq-count can be used.Thanks for the feedback. I'll roll another release for the sake of getting the latest fixes out to the world, and then see about replicating and documenting the process of creating the gene resource and cnv-expression correlates.
Much appreciated.
Do you have any suggestions for cleaning up the calls I'm getting? So far I've tried specifying normal samples, using --no-txlen
, --max-log2 2
, and segment -m none
. The PDFs I've attached are with 3 normal samples specified, using counts, and with the rest of the parameters default. The total input was 15 RNA seq samples. As you can see, the XY normal sample segments are still quite variable. In the -16 samples, there is a clear decrease in log2 for chrom 16. However in the XO samples there is no clear decrease in XO (this could be due to dosage compensation or the fact that the population contains both XX and XY samples). Any suggestions on how to bring the baseline closer to 0 and reduce variability? Thanks!
normal1.pdf normal2.pdf normal3.pdf XO-1.pdf XO-2.pdf XO-3.pdf minus16-1.pdf minus16-2.pdf minus16-3.pdf plus16-1.pdf
Thanks for your great tool and in advance for your help.