Summarizing info of mapped gapped reads in R

Question

[caggtaagtat]

Hi there,

Until now, I'm using the R package "rbamtools" for uploading my data in R for the analysis of gapped reads, however I was wondering, what packages or functions you use and recommend?

Edit of question titel:

From: How to best upload bam files in R for analysis of alternative splicing

To: Summarizing info of mapped gaped reads in R

[GenoMax]

Have you tried to google using a part of your post title (R for analysis of alternative splicing)? That flags R packages that can be of interest.

BTW: How to best upload bam files in R that part of the title does not seem to have direct relevance to the question you are asking.

[caggtaagtat]

I know, that there are other packages for that purpose, but I thought maybe someone, who is also interested in splicing, could share their prefered way to just upload/compress the data in R.

Since I'm only interested in ways to summarize the information of the gapped reads while importing them in my R workspace, I don't understand why my title would be misleading

[Chris Fields]

The question to me appears to be asking how to upload BAMs into R, not what packages in R are others using for alternative splicing.

[GenoMax]

share their prefered way to just upload/compress the data in R.

That isn't necessarily related to splicing per se, correct?

efficiently summarize the information of the gapped reads while importing them in my R workspace

Now that would be a much better title that succinctly describes what you are looking for.

[caggtaagtat]

Gapped reads of human mRNA almost completely originate from spliced transcripts, therefore the uploading/compressing step involves the summary of information about exon junctions e.g. the genomic position of the splice donor, the sequence of the splice acceptor or the intron length.

But to avoid confusion, it may be better to rename my question

[WouterDeCoster]

hi caggtaagtat,

There is no need to remove questions.

Cheers, Wouter