... | ... | @@ -187,8 +187,8 @@ The second part is either "all" or "unq": |
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- "all" counts reads that have aligned on multiple genes. The read count is assigned to the gene defined as the primary alignement in the bam files.
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- "unq" counts only the reads which align on one gene. Reads can align on multiple transcripts but of only one gene.
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The third part of the name defines the informations to be fount:
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- "log" is a summary of the counts for the whole run.
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The third part of the name defines the informations to be found:
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- "log" is a summary of the counts for the whole project.
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- "refseq" is the expression matrix. It is there that you will find all counts for each sample and for each gene.
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- "spike" is the count matrix of the spike-in. It is there for legacy reasons and is not used in our implementation of the technique.
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- "unknown_list" is the list of the tracks present in the fasta file (ie, the list of transcript) which are not assigned to a gene in the sym2ref file (ie, no annotation).
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