Finally, I was able to run SalmonTE using an amd64 system instead of arm64. I would like to see differences in TE expression after different treatments and have biological and technical replicates from paired-end bulk RNA seq data.
How should I deal with the technical replicates? do you recommend concatenating the fastq files (example: cat sample1_line1_R1.fastq.gz sample1_line2_R1.fastq.gz > sample1_R1_merged.fastq.gz) -same for R2- before running SalmonTE.py quant?
To test differential expression between conditions, should I run SalmonTE.py test per condition (--conditions= control, drug1) or there is a way to do all possible comparisons? --conditions= control, drug1, drug2, drug3?
Dear Hyun-Hwan Jeong,
Finally, I was able to run SalmonTE using an amd64 system instead of arm64. I would like to see differences in TE expression after different treatments and have biological and technical replicates from paired-end bulk RNA seq data.
How should I deal with the technical replicates? do you recommend concatenating the fastq files (example: cat sample1_line1_R1.fastq.gz sample1_line2_R1.fastq.gz > sample1_R1_merged.fastq.gz) -same for R2- before running SalmonTE.py quant?
To test differential expression between conditions, should I run SalmonTE.py test per condition (--conditions= control, drug1) or there is a way to do all possible comparisons? --conditions= control, drug1, drug2, drug3?
Example- condition.csv file SampleID Condition Sample1 drug1 Sample1 drug2 Sample1 drug3 Sample1 control Sample2 drug1 Sample2 drug2 Sample2 drug3 Sample2 control
Thanks in advance, Lorena