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FASDA-ABUNDANCE(1) General Commands Manual FASDA-ABUNDANCE(1) NAME fasda abundance - Compute abundances from SAM/BAM/CRAM data SYNOPSIS fasda abundance \ --debug \ --show-gene-name \ --ignore-chromosome-order \ --feature-type extended-RE \ --output-dir dir \ features.gff3 alignment-file [alignment-file ...] DESCRIPTION fasda abundance computes raw read counts from one or more SAM/BAM/CRAM files overlapping each features in a GFF3 file. Output is an abundance.tsv file in the same format as those produced by kallisto. Estimated counts may not match those produced by kallisto as they are calculated differ- ently. However, the ratio of kallisto counts / fasda counts should be fairly consistent, and the fold-changes produced by fasda fold-change should therefore be highly similar. The GFF3 and SAM/BAM/CRAM inputs must be sorted in the same order. By de- fault, sort order is checked for both input streams using bl_chrom_name_cmp(3), and fasda abundance aborts if either is out of order. If this check is disabled using --ignore-chromosome-order, and chromosomes in the inputs are not in the same order, fasda abundance may produce incor- rect output. Abundances in the output are raw counts of properly paired reads that aligned to a feature of the selected type, are not flagged as secondary, duplicate, or supplementary alignments, and did not fail QC. For paired- end reads, both mates are counted separately, so the counts should be ex- pected to reflect about double the number of fragments aligned. Any normalization of counts is left to downstream tools such as fasda-nor- malize(1). OPTIONS --debug Turn on debugging output --show-gene-name Show gene name rather than feature (mRNA/transcript) name in output. --ignore-chromosome-order Do not abort if GFF3 or SAM/BAM/CRAM input chromosomes are not sorted in order determined by bl_chrom_name_cmp(3). If this option is used, you must ensure that the order of the chromosomes is the same in the GFF3 and SAM/BAM/CRAM input. --feature-type extended-RE Indicate which feature types (column 3) in the GFF3 input each read should be checked for overlap with. This is an extended regular ex- pression (see regex(3)). The default is "RNA$|transcript$|gene_seg- ment$", i.e. any feature ending in "RNA", "transcript", or "gene_segment", such as "mRNA", "snRNA", "transcript", "uncon- firmed_transcript", etc. For Ensembl GFFs, this matches features of type "transcript" in the GTF, which is the default for some other tools, including kallisto and gffread. --output-dir directory Indicate where -abundance.tsv output files should go. The default is the same directory is the SAM/BAM/CRAM input. FILES features.gff3 alignment.bam SEE ALSO fasda-normalize(1), fasda-fold-change(1) BUGS Please report bugs to the author and send patches in unified diff format. (man diff for more information) AUTHOR J. Bacon FASDA-ABUNDANCE(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | FILES | SEE ALSO | BUGS | AUTHOR
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