I'm a newbie in R and RNA seq analysis, so don't judge me so much)
I'm trying to perform RNA-seq analysis as it says here http://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html , I was given a bunch of bam/bam.bai files(C33A and HeLa) 3 scrambled and 3 shoct4 files for each gene, so as a first step I need to do counts, here is the first question:
Should I use featurecounts functions for all bam files of one type of genes or parse them separately?
As others said in the comments above, pass all bam files to featureCounts, then its output will contain all counts in one file, which is simpler to parse. However, there should be no differences in counts, regardless you pass one file at a time or all files together.
I don't understand which differences between your and the tutorial counts are puzzling you: 1) the actual counts; 2) the column names; 3) the missing length column.
The actual counts are different because you and the tutorial are analysing different data sets: cancer cell lines (C33A and HeLa) versus "basal stem-cell enriched cells (B) and committed luminal cells (L) in the mammary gland of virgin, pregnant and lactating mice". By the way, are you using a human or mouse reference genome?
Column names can be easily changed with colnames( seqdata ) <- c( "name1", "name2", "name3" ).
And the length column can be additionally parsed from the featureCounts output file.