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changes.mady.by.user Micha Sammeth

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  1. Gene Models (annotation in GTF format), REQUIRED: if missing, the program responds with an error like

    Code Block
    Hey, you forgot to specify a valid input file!
This is a bit important, I cannot work without an input annotation. I want a GTF file with transcript annotations (exon features, with a mandatory optional attribute named 'transcript_id') IN THE SAME COLUMN (i.e., if the transcript identifier of the 1st line is in column #10, it has to be in all lines of the file in column #10. The rest of the file should comply with the standard as specified at http://mblab.wustl.edu/GTF2.html.

  2. Chromosome sequences (in atomary FASTA files) REQUIRED: if missing, the program responds with an error like

    Code Block
    [ERROR] Splice site scoring requires the genomic sequence, provide a value for parameter 'CHR_SEQ' in the parameter file, or via the command line flags -c or --chr!
    Warning

    The chromosome sequences currently have to be provided as separate files, one per chromosome. All of these files have to be in the same folder (e.g., genomes/H.sapiens/hg19) with a filename prefix that corresponds to the tags in column $1 of the GTF filel provided and a suffix ".fa" or ".fasta"; e.g., if chromosomes are named "chr1", "chr2", etc. then the program expects files named "chr1.fa", "chr2.fa", ...

    The first line of every

  3. Genetic variants (as

    a 

 

Basic Setup

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  1. a pseudo VCF file)

    Section

    Modified bases can be provided in a 5-column file format that resembles the variant-calling-format (VCF): column 1 is chromosome ID (number or letter), column 2 is position within the chromosome (integer), column 3 is variant identifier, column 4 is reference nucleotide and column 5 is the variant nucleotide.

    Code Block
    1	948921	rnaedit_1_948921	T	C
1	982994	rnaedit_1_982994	T	C
1	990773	rnaedit_1_990773	C	T
1	1158631	rnaedit_1_1158631	A	G
1	1247494	rnaedit_1_1247494	T	C
1	1309405	rnaedit_1_1309405	T	C
1	1336006	rnaedit_1_1336006	C	T
1	1336626	rnaedit_1_1336626	G	A
1	1342394	rnaedit_1_1342394	G	A
1	1684472	rnaedit_1_1684472	C	T