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PierreBSC / Viral-Track

MIT License
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What is "Viral_annotation_file" and "Single_cell_metadata"? #13

Closed yangjywhu closed 4 years ago

yangjywhu commented 4 years ago

Hello,

Viral-Track is a good software to treat the scRNA-seq data of virus infection. It is an important contribution. But I have some problems with it:

  1. What is Viral_annotation_file? You have provided in github, but I still don't know what I should prepare the file of mine.
  2. What is Single_cell_metadata?(in file Parameters.txt) I have seen nothing about it in tutorial. (may be I miss it) My data is a scRNA-seq of COVID-19 patients' pbmc. Maybe I can use some file of yours?
  3. Read2 is the only example in Files_to_process.txt, can I use Read1? Which should I use in this? (before umi_tools or after it) Look forward to your reply.

Best, Jiayi Yang

PierreBSC commented 4 years ago

Hi Jiayi,

Thank you for your positive feedback !

  1. This file contains a description of each viral chromosome and must have 4 different columns : one with the exact name/ID of the chromosome (Name_sequence), one with the length of the chromosome length (Genome_length), the name of the virus (Virus_name, as some viruses have multiple segments/chromosomes), the full name of the segment (Complete_segment_name, virus name + segment number). This is not optimal and will likely change in the coming months.
  2. Single_cell_metadata in the Parameters.txt file was used in previous versions of Viral-Track but is not used anymore, so you can remove it.
  3. Sure you can apply Viral-Track to any scRNA-seq technology / sequencing approach ! We have tested VT on various technologies, including MARS-seq, DROP-seq, 10X etc...

Hope this helped !

Best

Pierre

yangjywhu commented 4 years ago

Thank you! My problems has been solved. For question 1, do you means that I can (or should) use Viral_annotation_file you have provided?

Thanks, Jiayi Yang

PierreBSC commented 4 years ago

Hi Jiayi,

Concerning question 1 you need to use a a file that is suited to the viral database fasta file used to build your STAR index. Which database did you used, VirusSite or an other one ?

Best

Pierre

yangjywhu commented 4 years ago

Thanks, I use MN996528 (genome of SARS-CoV-2) to build STAR index. What should I use in Viral_annotation_file? Maybe a line of MN996528 is OK? (I only want to map to this genome)

PierreBSC commented 4 years ago

Hi Jiayi,

Sorry for the delay ! In theory it should do the job !

Best

Pierre

yangjywhu commented 4 years ago

Thank you @PierreBSC !

malonzm1 commented 1 year ago

Hi,

Re

  1. Read2 is the only example in Files_to_process.txt, can I use Read1? Which should I use in this? (before umi_tools or after it) Look forward to your reply.

Best, Jiayi Yang

Are R2 (coding) fastq files the only ones included in Files_to_process.txt?

Thanks and good day.