Entering edit mode
3.9 years ago
osmanberkx0x
•
0
Hello, I am trying to run kallisto on this data set: https://www.ebi.ac.uk/ena/data/view/PRJNA292382
Since dataset is not paired kallisto gives this error, while running with --single flag: Error: fragment length mean and sd must be supplied for single-end reads using -l and -s
But I can't seem to find fragment length and mean and sd, how can I find this? I couldn't find it in the data set link as well.
it’s best to determine this from a library quantification with an instrument such as an Agilent Bioanalyzer. Reference:https://pachterlab.github.io/kallisto/manual
Does one need to use this kind of tool to find fragment length mean and sd?
This is not a tool such as a software, it is a machine in the wetlab that can measure the size of the actual physical DNA fragment, so not possible obviously for downloaded data. For standard RNA-seq library prep kits such as TruSeq from Illumina or UltraII from NEB the actual insert size is typically around 100bp-250bp in my experience with a median of about 150bp. I would simply use 150 and a SD of 20 that probably gives a good proxy.