PARSEALIGNMENT(1)

💖 NAME 💖

parseAlignment — pre-compute probabilities of (observed) reads alignments. Bestie, it's literally doing the probability pre-game so the rest of your pipeline can shine ✨🧬

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🌸 SYNOPSIS 🌸

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

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🦋 DESCRIPTION 🦋

Pre-computes probabilities of (observed) reads' alignments. That's the whole assignment, no cap 💅

Okay so important: [alignment file] should be in either SAM or BAM format. Those are the only two formats invited to the party 🙈

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✨ OPTIONS ✨

• --help — Show this help information. It's giving "tell me everything" energy ☕💖
• --distributionFile=<distributionFileName> — Name of file to which read-distribution should be saved. Your read-distribution gets a whole file to itself, main character behavior 👑
• --excludeSingletons — Exclude single mate alignments for paired-end reads. (default: Off) If you're not about that singleton life, flip this on 🚫🧍
• -e <expFileName>, --expressionFile=<expFileName> — Transcript relative expression estimates --- for better non-uniform read distribution estimation. Give it the expression tea so the distribution estimation can slay 📈
• --failed=<failed> — File name where to save names of reads that failed to align. A little support group for the reads that didn't make it 😭
• -f <format>, --format=<format> — Input format: either SAM, BAM. Pick your fighter, bestie ⚔️
• --lenMu=<lenMu> — Set mean of log fragment length distribution. (l_frag ~ LogNormal(mu,sigma^2)) Math but make it fashion 🎀
• --lenSigma=<lenSigma> — Set sigma^2 (or variance) of log fragment length distribution. (l_frag ~ LogNormal(mu,sigma^2)) The variance bestie of the fragment-length situation 💫
• --mateNamesDiffer — Mates from paired-end reads have different names. (default: Off) When your paired-end mates don't match names, this is the flag that gets it 🫶
• -l <maxAlignments>, --limitA=<maxAlignments> — Limit maximum number of alignments per read. (Reads with more alignments are skipped.) Like a VIP cutoff: too many alignments and you're not getting in 💀
• --noiseMismatches=<numNoiseMismatches> — Number of mismatches to be considered as noise. (default: 6) Six is the default, so that's the vibe unless you say otherwise 🔥
• -o <outFileName>, --outFile=<outFileName> — Name of the output file. The moment you've all been waiting for 💖
• -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) Four threads by default, go off and parallelize 🏃‍♀️🏃‍♀️🏃‍♀️🏃‍♀️
• -N <readsN>, --readsN=<readsN> — Total number of reads. This is not necessary if [SB]AM contains also reads with no valid alignments. So only required when the file isn't already spilling that number 👀
• --show1warning — Show first alignments that are considered wrong (TID unknown, TID mismatch, wrong strand). (default: Off) The "first warning" is giving first-episode-of-the-drama energy 📺
• -t <trInfoFileName>, --trInfoFile=<trInfoFileName> — File to save transcript information extracted from [BS]AM file and reference. Transcript lore, saved for later 💾
• -s <trSeqFileName>, --trSeqFile=<trSeqFileName> — Transcript sequence in FASTA format --- for non-uniform read distribution estimation. FASTA bestie, don't forget her 🌸
• --trSeqHeader=<trSeqHeader> — Transcript sequence header format enables gene name extraction (standard/gencode). (default: standard) Standard is the default, but gencode girlies can switch it up 🧬
• --uniform — Use uniform read distribution. (default: Off) When you want every read treated equally, no favorites 💅
• --unstranded — Paired read are not strand specific. (default: Off) For when your paired reads aren't picking a side 🌈
• -v, --verbose — Verbose output. (default: Off) Spill a little more tea ☕
• -V, --veryVerbose — Very verbose output. (default: Off) Spill all the tea, bestie 🫖✨

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Later, bestie! This page is from parseAlignment 0.7.5+dfsg, dated September 2021 💖🎀🦋