I want to quantify the reads I have from several .bam files from Tophat.
I used two different annotations(one at a time):
1: CuffMerge generated GTF file;
2: UCSC genome annotation
I made a transcript data base by using Bioconductor package "GenomicFeature" function "makeTranscitpDbFromGFF" or "makeTranscitpDbFromUCSC"
Then I make a object that store the exon or transcripts information, by using Rsamtools package function "exonsBy" or "transcriptsBy"
Then I do the overlap between my .bam file and the previous object ("countOverlaps")
Anyone see any problems by doing what I did?
I took this as a reference:
Please let me know what could go wrong with this~
Thanks a lot!
I used two different annotations(one at a time):
1: CuffMerge generated GTF file;
2: UCSC genome annotation
I made a transcript data base by using Bioconductor package "GenomicFeature" function "makeTranscitpDbFromGFF" or "makeTranscitpDbFromUCSC"
Then I make a object that store the exon or transcripts information, by using Rsamtools package function "exonsBy" or "transcriptsBy"
Then I do the overlap between my .bam file and the previous object ("countOverlaps")
Anyone see any problems by doing what I did?
I took this as a reference:
Please let me know what could go wrong with this~
Thanks a lot!
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