Hi,

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?

Thanks,

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