I have hg38 coordinates at hand and I want to convert them to hg19 coordinates using
ncbi remap_api.pl in java.
Here is my perl remap arguments in a string array.
[perl , C:\\Users\\Burçak\\Google Drive\\Data\REMAP\remap_api.pl, --mode asm-asm , --from , GRCh38, --dest , GRCh37.p13, --annotation , chrName_0Based_StartInclusive_EndExclusive_hg38_coordinates.bed, --annot_out , chrName_0Based_StartInclusive_EndExclusive_hg19_coordinates.bed]
I'm executing these parameters in runtime and there is no output.
I just get the the following usage information. Any idea?
Usage: perl remap_api.pl Please limit your submissions to files of approximatly 250,000 rows, and at most 4 simultaneous submissions. --mode <mode> batches, asm-asm, asm-rsg, rsg-asm, alt-loci. batches will print a list of all assembly-assembly pairs that alignments exist for. batches use no other argumentes, other modes: asm-asm is for mapping between two assemblies asm-rsg is for mapping from an assembly to a gene data set (RefSeq or LRG) rsg-asm is for mapping from a gene data set to an assembly alt-loci is for mapping between a primary assembly and its related alt-loci required: --annotation <filename> The file containing your existing annotation (GFF3, GVF, BED, etc) --from <gencoll accession> --dest <gencoll accession> The gencoll accessions for the assemblies being mapped to and from Use 'RefSeqGene' when mapping to or from RefSeqGene Use 'LRG' when mapping to or from LRG Leave out --dest when use 'alt-loci' mode options: --allowdupes <'on' or 'off'> on (default) does all possible mappings, off excludes second pass mappings --merge <'on' or 'off'> on (default) will merge fragmented mappings back together off will leave fragmented results untouched --mincov <fraction 0.01 to 10.0, default 0.5 > --maxexp <fraction 0.01 to 10.0, default 2.0 > (r_cov = mapped_feature_length / original_feature_length if r_cov < min_cov then throw out feature if r_cov > max_exp then throw out feature ) mapped_feature_length might not be identical to original_feature_length because the mapping alignments are not always identical. Large gaps might be inserted into features, causing the total feature length to grow. Or regions covered by a feature might not be covered by alignments at all, so the mapped feature is smaller than the original --in_format <guess (default), hgvs, bed, gvf, gff, gtf, gff3, asnt, asnb, region> --out_format The input format of your annotation file, and the desired output format Conversions to different formats might not preserve meta-data exactly. Leave --out_format alone to get out the same format as in. Guess leaves the decision to our service. Exit status = 0