wrui / post_implantation

Post implantation analysis

post_implantation's Issues

Allele assignment of sequencing reads

Hi WangRui,
Recently, I met a quietly difficult problem about assigning sequencing reads from ChIPseq data to paternal or maternal genome. I have read the supplement of research article published by your team. But my data comes from two strains mouse. I don't know how to classify the reads into paternal and maternal reads. Can you illustrate the whole procedure and recommend some useful tools? I cannot get more help from my colleagues. So, I have to ask you about this question.
Hanwen Yu
Thank you sincerely!

Trying to align fastq files - UMI barcode position

Hello. I am currently trying to realign the raw data from this paper using the kallisto-bustools pipeline. I am able to specify custom technology by demarcating which read and the start and end position of the barcode and UMI. However, when I am trying to align it, the output is not giving the outcome of barcodes expected based on the deposited .txt files. Can you clarify the formating of the files and position of the barcode and UMI in them?

About PBAT jobs

Hello WRui,

I am very pleased to see your work in the literature and I read your code carefully, I noticed that the singleC_metLevel.hg19.pl is missing.

so I would like to know if you can add this code here?

Thanks a ton!

raw count data

Dear WRui,

I came across your work in your Nature 2019 paper (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109555). Really great stuff! We'd like to include your dataset in a study of network evolution through embryological development. On the GEO you've already posted the TPM matrix, but for our purposes we need the raw count data. Would it be possible to share that with us?

Thanks a lot!

All the best,
Celine

Region_Ave_MethRatio.R missing

Hello Rui @WRui

I noticed that the Region_Ave_MethRatio.R is missing.

so I would like to know if you can add this code here?

Thanks !

about ChangeReadID.pl

Hello WRui,
I am very pleased to see your work in the literature and I read your code carefully, I noticed that the ChangeReadID.pl is missing. So can you add this code to this project?
Thanks a lot!

why bismark_v0.7.6 ?

The bismark software is so old for v0.7.6

why remain use that old version?

And some script like singleC_metLevel.hg19.pl do not exists!