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)