The analysis pipeline for Pacbio sequencing data analysis and its applications

[sunhaocuhk]

Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer

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Phase I Build the analysis pipeline for Pacbio sequencing data analysis for WGS, RNA and DNA methylation with docker image and cluster computing.

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2024.05.28 Try to run a hifisomatic workflow in the HPC with singularity and miniwdl. But there are some errors need to be figure out. For this workflow, it can output Whole-genome copy number profile, Small variants (SNV/INDEL) coverage and variant allele frequency (VAF) distribution, Mutational signatures, Table of filtered SNVs/INDELs, Table of filtered SVs and Differentially methylated regions overlapping with promoters. Its input file include tumor.bam and normal.bam for each patients. And it provide two big datasets : full COLO829 and HCC1395 dataset . COLO829 (60X tumor, 60X normal): https://downloads.pacbcloud.com/public/revio/2023Q2/COLO829 HCC1395 (60X tumor, 40X normal): https://downloads.pacbcloud.com/public/revio/2023Q2/HCC1395

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6.04

Roughly used the LaTeX format and synchronized it to GitHub

Try to run a hifisomatic workflow in the NGS cluster with singularity and miniwdl. I move the Conda's pkgs to /data Hard Disk resolving the issue of lack of space in home directory. In NGS cluster, I can run singularity. But there are still some errors . docker: "quay.io/pacbio/purple@sha256:8f9a70a1e3c6ee86b5cf41ec31fdc90c7cca744f35d84cd9caa997833245e61d" This image in quay.io is not working, so I plan to try other platforms to search such images. Therefore, the subsequent CNV analysis also cannot work.

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6.12 Last week the problem I met : unauthorized docker image named purple "quay.io/repository/pacbio/purple" now is authorized, so I pulled the docker image successfully.

The cnv task had some problems. My reference genome fasta is already indexed. cnkit.py is attempting to re-create this file and failing. I searched for many solutions, but I still couldn't solve the problem until I found an issue on GitHub's cnvkit issues page that had the same issue as mine. The solution : Updating the timestamp did the trick.

Then I met the problem: No space left on device. I checked the hard disk usage and found that indeed the /share/ directory had no space left. So, I copied all the data to the /data/ directory to try again.

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6.19 I ran the complete COLO829 dataset through this pipeline. When calling small variants, I initially used the deep somatic software, but it was computationally expensive and ran for almost two days, still resulting in errors for two contigs. Therefore, I switched to ClairS software, which is more time-efficient compared to deep somatic, but its image was difficult to pull, and I had to try multiple times to successfully do so. The ClairS software is still running. The ClairS software is still running.

[XH-BIM]

7.4 I successfully ran the complete HCC1395 (60X tumor, 40X normal) and COLO829 (60X tumor, 60X normal) datasets through the pipeline and got their reports.