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Gene Models (annotation in GTF format), REQUIRED: if missing, the program responds with an error like
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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. |
Chromosome sequences (in atomary FASTA files) REQUIRED: if missing, the program responds with an error like
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[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! |
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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 |
Genetic variants (as
a
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a pseudo VCF file)
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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. |
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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 |