differentially expressed genes

Question

[bioinfo]

Can anyone please tell me how to run sam in r?? i am bit confused. Thanks in advance.

[Thibault D.]

Hi,

What do you mean exactly when you say "run sam in r" ? Do you want to open it in RScript ? Do you want a SAM-Format parser in RScript ?

Answer 1

[Antonio R. Franco]

You have several choices

1. If doing RNA-Seq, you can directly use SAM/BAM files with the R package BitSeq. In one of the latest publications, this package is evaluated like one of the finest. Read the vignette to learn how to use it
2. You can extract information about your SAM/BAM file with tools like HTSeq-count, etc, and then use R with programs like DESeq2, edgeR, NOISeq, etc