parseAlignment - pre-compute probabilities of (observed) reads
alignments
parseAlignment -o <outFileName> -s
<trSeqFileName> [OPTIONS] [alignment file]
Pre-computes probabilities of (observed) reads' alignments.
- [alignment file] should be in either SAM or BAM format.
--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)