HT-seq CPTAC,RNA-seq

Question

[Rob]

Hi friends I am trying to download HT-seq CPTAC RNA-seq for kidney and there is no HT-seq in the workflow section. Instead there is star-count. So, my python code does not work and cannot get the HT-seq.

Where is the HT-seq count and what should I do?

Here is the image and link for CPTAC-3:

https://portal.gdc.cancer.gov/repository?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22kidney%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22CPTAC-3%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.experimental_strategy%22%2C%22value%22%3A%5B%22RNA-Seq%22%5D%7D%7D%5D%7D&searchTableTab=cases

[dsull]

Why do you need HT-seq? The current official GDC pipeline gives you the counts from STAR directly -- just use those.

[Rob]

Thanks I dont know how to download STAR then. it gives one file for each patient, but I need them together as one big file. I have a python script for the HT-seq count to merge them while downloading, but it does not work for STAR.

Is there any python or R script to download and merge STAR?

[dsull]

Modify your existing python code to get it to work for the STAR - Counts files.

Consider that your homework. :)

[Rob]

Sorry I have no idea about coding and python That is why I asked my Q here to see if anyone can help.

[dsull]

Sorry, but we aren't going to write code for you. We can help you figure out errors in your code but we aren't going to do your work for you.

I recommend you either learn python or you ask someone at your workplace who's willing to do coding work for you (e.g. if you're working at a university, contact a bioinformatics core facility member).

There are people who work full time (and get paid) doing these things; people on biostars are not such people.