bionic (1) conv_gtf_to_bed.1.gz

NAME

       conv_gtf_to_bed - legacy script for invoking the PALEOMIX command "gtf_to_bed"

SYNOPSIS

       paleomix gtf_to_bed [options] in.gtf out_prefix [in.scaffolds]

DESCRIPTION

       The  PALEOMIX  pipelines  are  a set of pipelines and tools designed to aid the rapid processing of High-
       Throughput Sequencing (HTS) data: The BAM pipeline  processes  de-multiplexed  reads  from  one  or  more
       samples,  through sequence processing and alignment, to generate BAM alignment files useful in downstream
       analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference  on  BAM  alignment
       files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out
       a suite of analyses on low coverage equine alignments, in order to detect the presence of  F1-hybrids  in
       archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts.

       The  pipelines  have  been  designed  with  ancient  DNA  (aDNA)  in  mind, and includes several features
       especially useful for the analyses of ancient samples, but can  all  be  for  the  processing  of  modern
       samples, in order to ensure consistent data processing.

       conv_gtf_to_bed is a legacy script for invoking the paleomix(1) command "gtf_to_bed"

OPTIONS

   positional arguments:
       INPUT.gtf
              Input file in GTF format.

       OUTPUT_PREFIX
              Prefix of output files.

       SCAFFOLDS
              Mapping of scaffolds to contig positions; e.g. mapping individual Un* scaffolds onto chrUn.

   optional arguments:
       -h, --help
              show this help message and exit

       --keep-all-transcripts
              Include  all  transcripts  in  the  output BED files, not just the longest transcript of each gene
              [default: off]

       --keep-malformed-proteins
              Include transcripts of protein-coding in the output, even if the the length  of  the  CDS  is  not
              divisible by 3 [default: off]

       --contig-prefix CONTIG_PREFIX
              Add prefix to contig names (e.g. 'chr') [default: no prefix].

SEE ALSO

       paleomix(1)

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.