Checking workflow for assembly of time series expt using Stringtie-Ballgown
0
0
Entering edit mode
10 months ago
nattzy94 ▴ 20

I have 2 timepoints (0h and 56h) and 5 replicates per timepoint.

Starting with 10 Bam files, my workflow is to :

  1. Run Stringtie on each Bam individually, giving me a total of 10 GTF files.
  2. I then merge the 5 individual GTF files of each timepoint so that I get 2 files: 0h_merged.gtf and 56h_merged.gtf.
  3. Run Stringtie again on the aligned bam files but this time using the respective merged file as the reference and also setting the -B and -e flags to generate the input files for DE analysis in Ballgown.

However, after reading this post, I'm not sure if I'm doing things right. From what I understand, the correct method should be to merge all 10 GTFs from step 1 into a single all_merged.gtf followed by running Stringtie again using all_merged.gtf as reference. Hence the workflow should be:

  1. Run Stringtie on each Bam individually, giving me a total of 10 GTF files.
  2. Merge all 10 GTF files into a single all_merged.gtf.
  3. Run Stringtie on the Bam files using all_merged.gtfas reference and -B and -e flags set.

Appreciate if someone could tell me which of these methods is correct?

RNA-Seq assembly • 175 views
ADD COMMENT

Login before adding your answer.

Traffic: 2158 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6