jefftc
commented
1 month ago Hi Sara,
Thanks for your email. At first look, I think you've identified some issues. Let me take a closer look at this, and I'll get back to you.
Jeff
On Jun 28, 2024, at 6:09 AM, saracosta261299 @.***> wrote:
Hello, First of all, thank you for the very nice tool you have created; it has been very useful in my research! I would like to ask for your assistance with a couple of issues I've encountered: Rule merge_samples_to_pseudobulk I'm noticing that the input for this rule is a file with the sample name repeated multiple times (corresponding to the number of batches, in my case 297). This seems incorrect, as I believe there should only be one input file when there is only one sample (name_sample.bam) and the output should be name_sample.merged.bam, which would be the same as the input in cases where there is only one sample. This current behavior not only leads to potential discrepancies in results but also significantly slows down the pipeline. To circumvent this, I've been skipping this rule, but I realize this won't be feasible when processing multiple samples together. Do you also have this problem when running the pipeline? Reproducing Results from N87 Cancer Cell Line I have run the pipeline on data from the N87 cancer cell line, as done in your published paper. However, I am not obtaining the same variants as those listed in your supplementary table, despite using the default parameters for mutation calling. I've attached the final genotypes.txt file I obtained for this N87 sample. Could you please verify if this matches your results? If not, do you have any suggestion for potential reasons for the discrepancy? Additionally, your paper mentions validation through clonal analysis. Could you share the clonal annotations for this dataset? Ideally, a dictionary with each of the four clones as keys and a list of corresponding cell barcodes would be extremely helpful. If you need any further clarification to address these issues, please let me know. Thank you in advance for your time and help, Sara Costa genotypes.txt — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>
saracosta261299
Hello,
First of all, thank you for the very nice tool you have created; it has been very useful in my research!
I would like to ask for your assistance with a couple of issues I've encountered:
Rule merge_samples_to_pseudobulk
I'm noticing that the input for this rule is a file with the sample name repeated multiple times (corresponding to the number of batches, in my case 297). This seems incorrect, as I believe there should only be one input file when there is only one sample (name_sample.bam) and the output should be name_sample.merged.bam, which would be the same as the input in cases where there is only one sample. This current behavior not only leads to potential discrepancies in results but also significantly slows down the pipeline. To circumvent this, I've been skipping this rule, but I realize this won't be feasible when processing multiple samples together. Do you also have this problem when running the pipeline?
Reproducing Results from N87 Cancer Cell Line
I have run the pipeline on data from the N87 cancer cell line, as done in your published paper. However, I am not obtaining the same variants as those listed in your supplementary table, despite using the default parameters for mutation calling. I've attached the final genotypes.txt file I obtained for this N87 sample. Could you please verify if this matches your results? If not, do you have any suggestion for potential reasons for the discrepancy? Additionally, your paper mentions validation through clonal analysis. Could you share the clonal annotations for this dataset? Ideally, a dictionary with each of the four clones as keys and a list of corresponding cell barcodes would be extremely helpful.
If you need any further clarification to address these issues, please let me know. Thank you in advance for your time and help,
Sara Costa genotypes.txt