I upload my datasets, into two collections; treated and control using “Download and Extract Reads in FASTQ format from NCBI SRA”.
I am performing RNA-Seq with paired-end dataset.
How do I rename the read files after uploading?
As all tutorials recommend mapping and performing features-count using a collection where all the paired-end read files are together. I need to change the names, to be able to identify them for the later steps.
Also, is it possible to perform mapping and gene-counting steps for the treated and control collections separately, as towards the end DSeq2 provides an option to select separate counts files (control and treated)?
Will it affect the outcome of the analysis, incase renaming isn’t possible?
Hi @Sanjukta_Ghosh
For a file, click at Edit Attributes (pencil icon) > Change name in the middle window and click Save.
For collections try Relabel identifiers (should be in Collection Operations section). You need a list of new names.
Yes, generally you can process experiment and control counts separately. Make sure the output files got all genes, including the ones with zero counts. Also, use the same version of tools and identical reference data. For tool version, maybe consider using re-run option: clicking on a tool in the tool panel brings the latest version of software. You should get exactly the same read counts, so the results will be the same. Personally, I prefer individual datasets over collections. Sometime I see sporadic job failure when jobs were submitted over a big collection. I also recommend Galaxy workflows with output renaming, so you can propagate the original names.
It is a matter of personal preferences.
Kind regards,
Igor
