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cuhk-haosun / course-MBI6013

Material for Msc. research project MBI6013
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Integratedly analyze data from nanopore to classify prostate cancer and normal #1

Closed MeowBing closed 2 weeks ago

MeowBing commented 3 months ago
MeowBing commented 3 months ago
  1. 可行性研究：收集公开数据，别人用nanopore做出了什么数据、应用cnv/sv/methylation分类的方法，excel表收集
  2. CNV、SV、methylation call出来的过程学习
  3. 数据分析过程：明白nanopore的long-reads数据的DEG方法，选定feature，要绘制哪些图
  4. discussion
MeowBing commented 2 months ago

image 两个大文件解压都遇到这个情况，请问可以怎么解决 @Milokita

Milokita commented 2 months ago

你数据下载完成后校验通过了吗？如果没有那就是文件下载不完整

MeowBing commented 2 months ago

image

长这样 @Milokita

Milokita commented 2 months ago

如果是如此，那你可能需要搜索一下如何忽略错误强制解压出来。 同时，在新的文件夹里重新下载看看

MeowBing commented 2 months ago

下载还是重新解压啊 @Milokita

Milokita commented 2 months ago

下载还是重新解压啊 @Milokita

双管齐下

MeowBing commented 2 months ago

按照原作者提供的下载方法下载了，校验码和原作者提供的一致，成功解压了run2.tar.gz具体内容如下： image

现准备重新下载run1

MeowBing commented 2 months ago

image run1的不知道为什么还是和官方的不一样，还要重下一次。。。。 @Milokita

Milokita commented 2 months ago

你链接发我 我HK给你下

MeowBing commented 2 months ago

wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR439/ERR4395307/run1.tar.gz这是官方的，然后这是校验码：<FILE checksum="766ae3c28f3007507d82aa73512bec7d" checksum_method="MD5" @Milokita

MeowBing commented 4 weeks ago
462fab4cbb413e9056171d4a289c575

目前进度：暂定自动运行脚本里面的命令可以正常运行 遇到问题：兴哥，我用sandbox运行容器后，好像只能使用宿主机上的文件（也就是NGS上的），不能用容器里面自带的？这是为什么？但是我想把reference.fa放在容器内部，方便自动化运行，所以是要在Dockerfile的时候加什么配置吗 @Milokita

Milokita commented 4 weeks ago

in general, it is not recommended to put large file such as ref in the docker

MeowBing commented 4 weeks ago

OK .Can I add code to yml to manually set the path to the reference file? @Milokita

Milokita commented 4 weeks ago

OK .Can I add code to yml to manually set the path to the reference file? @Milokita

To be specific, you should download the ref in NGS cluster and passed it into the container when running the container

MeowBing commented 4 weeks ago

After setting up my path, I encountered this situation. image Is there anything else I need to set before "run on"? Please check out my public library minimap2，Thank you @Milokita

Milokita commented 3 weeks ago

You should create the rest repo inside cuhkhaosun group to use our worker.

MeowBing commented 3 weeks ago

image image image

I modified the code according to yesterday's suggestion, but it seems that I still stay in this interface, I don't know why? Please take a look at it,thank you! @Milokita @xxx58

Milokita commented 3 weeks ago

The problem should be fixed now, pls open new issue if you have question, this issue is mainly for progress report

MeowBing commented 2 weeks ago

[Uploading 20240611-weekly report.pptx…]()

Milokita commented 2 weeks ago

do not upload the file here, use pr