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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 abun- dance.tsv file in the same format as those produced by kallisto. Esti- mated counts may not match those produced by kallisto as they are cal- culated differently. 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 default, 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 incorrect 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 sec- ondary, duplicate, or supplementary alignments, and did not fail QC. For paired-end reads, both mates are counted separately, so the counts should be expected to reflect about double the number of fragments aligned. Any normalization of counts is left to downstream tools such as fasda- normalize(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 op- tion 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 expression (see regex(3)). The default is "RNA$|tran- script$|gene_segment$", i.e. any feature ending in "RNA", "tran- script", or "gene_segment", such as "mRNA", "snRNA", "tran- script", "unconfirmed_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 de- fault 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 for- mat. (man diff for more information) AUTHOR J. Bacon FASDA-ABUNDANCE(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | FILES | SEE ALSO | BUGS | AUTHOR
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