Man page - parsealignment(1)
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Manual
PARSEALIGNMENT
NAMESYNOPSIS
DESCRIPTION
OPTIONS
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
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--help |
Show this help information.
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--distributionFile= <distributionFileName> |
Name of file to which read-distribution should be saved.
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--excludeSingletons |
Exclude single mate alignments for paired-end reads. (default: Off)
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-e <expFileName> , --expressionFile= <expFileName> |
Transcript relative expression estimates --- for better non-uniform read distribution estimation.
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--failed= <failed> |
File name where to save names of reads that failed to align.
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-f <format> , --format= <format> |
Input format: either SAM, BAM.
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--lenMu= <lenMu> |
Set mean of log fragment length distribution. (l_frag ˜ LogNormal(mu,sigmaˆ2))
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--lenSigma= <lenSigma> |
Set sigmaˆ2 (or variance) of log fragment length distribution. (l_frag ˜ LogNormal(mu,sigmaˆ2))
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--mateNamesDiffer |
Mates from paired-end reads have different names. (default: Off)
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-l <maxAlignments> , --limitA= <maxAlignments> |
Limit maximum number of alignments per read. (Reads with more alignments are skipped.)
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--noiseMismatches= <numNoiseMismatches> |
Number of mismatches to be considered as noise. (default: 6)
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-o <outFileName> , --outFile= <outFileName> |
Name of the output file.
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-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)
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-N <readsN> , --readsN= <readsN> |
Total number of reads. This is not necessary if [SB]AM contains also reads with no valid alignments.
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--show1warning |
Show first alignments that are considered wrong (TID unknown, TID mismatch, wrong strand). (default: Off)
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-t <trInfoFileName> , --trInfoFile= <trInfoFileName> |
File to save transcript information extracted from [BS]AM file and reference.
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-s <trSeqFileName> , --trSeqFile= <trSeqFileName> |
Transcript sequence in FASTA format --- for non-uniform read distribution estimation.
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--trSeqHeader= <trSeqHeader> |
Transcript sequence header format enables gene name extraction (standard/gencode). (default: standard)
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--uniform |
Use uniform read distribution. (default: Off)
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--unstranded |
Paired read are not strand specific. (default: Off)
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-v , --verbose |
Verbose output. (default: Off)
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-V , --veryVerbose |
Very verbose output. (default: Off)