NAME

       parseAlignment - pre-compute probabilities of (observed) reads alignments

SYNOPSIS

       parseAlignment -o <outFileName> -s <trSeqFileName>  [OPTIONS] [alignment file]

DESCRIPTION

       Pre-computes probabilities of (observed) reads' alignments.

              [alignment file] should be in either SAM or BAM format.

OPTIONS

       --help

              Show this help information.

       --distributionFile=<distributionFileName>

              Name of file to which read-distribution should be saved.

       --excludeSingletons

              Exclude single mate alignments for paired-end reads. (default: Off)

       -e <expFileName> ,   --expressionFile=<expFileName>

              Transcript   relative   expression   estimates  ---  for  better  non-uniform  read
              distribution estimation.

       --failed=<failed>

              File name where to save names of reads that failed to align.

       -f <format> ,   --format=<format>

              Input format: either SAM, BAM.

       --lenMu=<lenMu>

              Set mean of log fragment length distribution. (l_frag ~ LogNormal(mu,sigma^2))

       --lenSigma=<lenSigma>

              Set  sigma^2  (or  variance)  of  log  fragment  length  distribution.  (l_frag   ~
              LogNormal(mu,sigma^2))

       --mateNamesDiffer

              Mates from paired-end reads have different names. (default: Off)

       -l <maxAlignments> ,   --limitA=<maxAlignments>

              Limit  maximum  number  of  alignments  per  read.  (Reads with more alignments are
              skipped.)

       --noiseMismatches=<numNoiseMismatches>

              Number of mismatches to be considered as noise. (default: 6)

       -o <outFileName> ,   --outFile=<outFileName>

              Name of the output file.

       -P <procN> ,   --procN=<procN>

              Maximum number of threads to be used.  This  provides  speedup  mostly  when  using
              non-uniform read distribution model (i.e. no --uniform flag). (default: 4)

       -N <readsN> ,   --readsN=<readsN>

              Total  number of reads. This is not necessary if [SB]AM contains also reads with no
              valid alignments.

       --show1warning

              Show first alignments that are considered wrong (TID unknown, TID  mismatch,  wrong
              strand). (default: Off)

       -t <trInfoFileName> ,   --trInfoFile=<trInfoFileName>

              File to save transcript information extracted from [BS]AM file and reference.

       -s <trSeqFileName> ,   --trSeqFile=<trSeqFileName>

              Transcript   sequence  in  FASTA  format  ---  for  non-uniform  read  distribution
              estimation.

       --trSeqHeader=<trSeqHeader>

              Transcript sequence header format enables gene name extraction  (standard/gencode).
              (default: standard)

       --uniform

              Use uniform read distribution. (default: Off)

       --unstranded

              Paired read are not strand specific. (default: Off)

       -v ,   --verbose

              Verbose output. (default: Off)

       -V ,   --veryVerbose

              Very verbose output. (default: Off)