I was looking for a way for specifying replicates in rsem-calculate-expression and bumped into your videos (you teach on youtube I guess!). So why not asking here... So if I wanna tell RSEM which sets of files (fastq's) are replicates, is there an option that allows to do that?

@mikevandewege3007

3 жыл бұрын

I don't think you would do that or rsem can recognize replicates. I could be wrong though. I think you would run rsem on your replicates independently, then label replicates in downstream analyses.

@vittoriozanzani9673

3 жыл бұрын

@@mikevandewege3007 ok that makes sense... thank you!

Hi. I am kind of new working with RSEM data. I am planning on doing some analysis in r. I have over 50 rsem files that I need to work with combined. How do I work with it or do I combine the data (if so how would I do it). Please and thank you

@mikevandewege3007

2 жыл бұрын

Hey Beverly, yea that's a bit of an annoying problem. You can use the R library tximport to import the read counts from each file into a matrix. I kind of described in DESeq pt 1 in this playlist (Bioinformatics Spring 2020). Also described here: bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#tximport. Alternatively, I use python to extract the read count columns from each file and build the matrix.