Difference between revisions of "Shore idtrans"
From SHORE wiki
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Required is either a ''*.trans'' file which is stored in the ''[[IndexFolder]]'' by ''shore preprocess'', or a ''ref.txt'' file generated by ''shore mapflowcell''. | Required is either a ''*.trans'' file which is stored in the ''[[IndexFolder]]'' by ''shore preprocess'', or a ''ref.txt'' file generated by ''shore mapflowcell''. | ||
| + | ==Command line options== | ||
'''Usage:''' shore idtrans [OPTIONS] FILES | '''Usage:''' shore idtrans [OPTIONS] FILES | ||
Latest revision as of 10:09, 28 September 2011
SHORE uses numerical identifiers for all sequences of the reference. shore idtrans simplifies translating these numbers in some of the result files back into chromosome names as specified in the reference fasta file (and vice versa).
Required is either a *.trans file which is stored in the IndexFolder by shore preprocess, or a ref.txt file generated by shore mapflowcell.
Command line options
Usage: shore idtrans [OPTIONS] FILES
| Allowed options | ||
| -t, --transfile=<arg> | *.trans file from IndexFolder | |
| -r, --reffile=<arg> | ref.txt file generated by mapflowcell | |
| -o, --outfile=<arg> | Output file (default: <infile>.idtrans) | |
| -c, --columns=<arg[,...]> | (Default: chr) | Columns to be translated (column names or @<column_number>) |
| --name2id | Translate names to IDs (default: translate IDs to names) | |
| --nocompress | Do not compress output files | |
