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cuffgtf2sam

Convert GTF files to SAM files

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Syntax

cuffgtf2sam(input,output)
cuffgtf2sam(input,output,Name,Value)

Description

cuffgtf2sam(input,output) converts the assembled transcripts in the GTF file input to the SAM-format file output [1].

cuffgtf2sam requires the Cufflinks Support Package for the Bioinformatics Toolbox™. If the support package is not installed, then the function provides a download link. For details, see Bioinformatics Toolbox Software Support Packages.

example

cuffgtf2sam(input,output,Name,Value) uses additional options specified by one or more name-value pair arguments. For example, gtf2sam('hum37_2_1M.gtf','hum37_2_1M.sam','UseFPKM',true) inserts the FPKM value into the SAM records.

Examples

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Convert a GTF file to a SAM file.

cuffgtf2sam('hum37_2_1M.gtf','hum37_2_1M.sam')

Input Arguments

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Names of input files, specified as a string, character vector, string vector, or cell array of character vectors.

Example: 'gyrAB.gtf'

Data Types: cell | char | string

Output SAM file name, specified as a string or character vector.

Example: 'gyrAB.sam'

Data Types: char | string

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

Example: gtf2sam('hum37_2_1M.gtf','hum37_2_1M.sam','UseFPKM',true)

Name of a reference FASTA file, specified as a string or character vector. If you specify a FASTA file, the function recreates the sequences of transcripts by comparing to the reference sequences in the provided FASTA file. If you do not specify 'ReferenceFASTA', the function omits the sequence information from the output SAM file.

Example: 'ReferenceFASTA',"ref.fasta"

Data Types: char | string

Flag to insert the FPKM value into the SAM records instead of the isoform fraction, specified as true or false.

Example: 'UseFPKM',true

Data Types: logical

References

[1] Trapnell, Cole, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, and Lior Pachter. “Transcript Assembly and Quantification by RNA-Seq Reveals Unannotated Transcripts and Isoform Switching during Cell Differentiation.” Nature Biotechnology 28, no. 5 (May 2010): 511–15.

[2] Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. “The Sequence Alignment/Map Format and SAMtools.” Bioinformatics 25, no. 16 (August 15, 2009): 2078–79.

Version History

Introduced in R2019a

See Also

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