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- We scan through each of the BAM files and find all the transcripts that have meet the minimum coverage threshold.
- With those transcripts, we "create" an annotation file that has the transcript name as the sequence name and the gene_id and transcript_id Gene ID and the Transcript ID have the same transcript name. The start position is 1 and the end position is the length of the transcript.
- Effectively, what the annotation file does is filter out the low coverage transcripts.
- Note that since Since we don't know where the transcripts are in the genome, chromosome view will display only one transcript at a time (i.e., the transcript names are treated like "chromosomes").
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Overview
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