Tweet
Hello. I'm trying to merge transcript.gtf I got from using cufflinks. Can someone explain how to make the assemblies.txt file
-
-
You can make the assemblies.txt file using an editor such that it contains paths (relative or full) to the transcripts.gtf files generated by cufflinks runs.
If you followed the same logic as described in the "Nature protocols" paper these would be in the "sample_ID_clout" folder.
You get the idea.Code:$ more assemblies.txt /path_to/sample1_clout/transcripts.gtf /path_to/sample2_clout/transcripts.gtf /path_to/sample3_clout/transcripts.gtf /path_to/sample4_clout/transcripts.gtf /path_to/sample5_clout/transcripts.gtf
-
So... If I have two transcript.gtf files I use what command? Just more assemblies.txt?Comment
-
You put the locations (file paths) of those two transcript.gtf files inside a single file and call that file "assemblies.txt".
Assemblies.txt file should contain file locations of all transcripts.gtf files you are trying to merge.Comment
-
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...05-06-2024, 07:48 AM -
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM
Comment