SUBJUNC(1)

💖 NAME 💖

subjunc — bestie, it's a whole toolkit for processing next-gen sequencing data. That's the manual name right there: SUBJUNC(1), and yeah, we're about to get into it. 🧬✨

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🎀 DESCRIPTION 🎀

Okay so first thing, the version, no cap:

Version 2.0.4

Usage, and yes you literally run it like this:

./subjunc [options] -i <index_name> -r <input> -o <output>

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✨ Mandatory arguments ✨

These ones you cannot skip, they're the main characters, periodt.

• -i <index> — Base name of the index. Just the base name, bestie. 💅
• -r <string> — Name of an input read file. Now listen: if you're doing paired-end, this is the first read file (typically the one with "R1" chillin' in the file name) and the second one goes in through -R. Acceptable formats include gzipped FASTQ, FASTQ, gzipped FASTA and FASTA. And the way it just knows which one you gave it — these formats are identified automatically. Iconic. 🦋

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🌸 Optional arguments: input reads and output 🌸

• -o <string> — Name of an output file. By default the output is in BAM format. And if you just... omit this option entirely? The output gets written to STDOUT. Surprise, bestie. 😭
• -R <string> — Name of the second read file in paired-end data (typically the one with "R2" in the file name).
• --SAMinput — Input reads are in SAM format.
• --BAMinput — Input reads are in BAM format.
• --SAMoutput — Save mapping results in SAM format.

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💜 Phred offset 💜

• -P <3:6> — Offset value added to the Phred quality score of each read base. '3' is for phred+33 and '6' is for phred+64. And '3' is the default, so you don't even gotta say anything.

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⭐ thresholds for mapping ⭐

• -n <int> — Number of selected subreads, 14 by default.
• -m <int> — Consensus threshold for reporting a hit (minimal number of subreads that map in consensus). If paired-end, this gives the consensus threshold for the anchor read (the anchor read receives more votes than the other read in the same pair). 1 by default.
• -p <int> — Consensus threshold for the non-anchor read in a pair. 1 by default.
• -M <int> — Maximum number of mis-matched bases allowed in each reported alignment. 3 by default. And lowkey important: mis-matched bases found in softclipped bases are not counted. 🙈

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🍓 unique mapping and multi-mapping 🍓

• --multiMapping — Report multi-mapping reads in addition to uniquely mapped reads. Use -B to set the maximum number of equally-best alignments to be reported.
• -B <int> — Maximum number of equally-best alignments to be reported for a multi-mapping read. Equally-best alignments have the same number of mis-matched bases. 1 by default.

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🔥 indel detection 🔥

• -I <int> — Maximum length (in bp) of indels that can be detected. 5 by default. But the range though — indels of up to 200bp long can be detected. Ate. 👑
• --complexIndels — Detect multiple short indels that are in close proximity (they can be as close as 1bp apart from each other). It's giving detail-oriented.

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🎀 read trimming 🎀

• --trim5 <int> — Trim off <int> number of bases from the 5' end of each read. 0 by default.
• --trim3 <int> — Trim off <int> number of bases from the 3' end of each read. 0 by default.

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🦋 distance and orientation of paired end reads 🦋

• -d <int> — Minimum fragment/insert length, 50bp by default.
• -D <int> — Maximum fragment/insert length, 600bp by default.
• -S <ff:fr:rf> — Orientation of first and second reads, 'fr' by default (forward/reverse).

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💅 number of CPU threads 💅

• -T <int> — Number of CPU threads used, 1 by default.

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🌈 read group 🌈

• --rg-id <string> — Add read group ID to the output.
• --rg <string> — Add <tag:value> to the read group (RG) header in the output.

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✨ read order ✨

• --keepReadOrder — Keep the order of reads in BAM output the same as that in the input file. And heads up bestie: reads from the same pair are always placed next to each other no matter whether this option is specified or not. So this one's just about the rest of 'em.
• --sortReadsByCoordinates — Output location-sorted reads. This option is applicable for BAM output only. A BAI index file is also generated for each BAM file so the BAM files can be directly loaded into a genome browser. Obsessed, honestly. 🫶

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💜 color space reads 💜

• -b — Convert color-space read bases to base-space read bases in the mapping output. But note, and this is the sneaky part: read mapping is performed at color-space. 👀

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🧚 dynamic programming 🧚

• --DPGapOpen <int> — Penalty for gap opening in short indel detection. -1 by default.
• --DPGapExt <int> — Penalty for gap extension in short indel detection. 0 by default.
• --DPMismatch <int> — Penalty for mismatches in short indel detection. 0 by default.
• --DPMatch <int> — Score for matched bases in short indel detection. 2 by default.

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💖 detect all junctions including gene fusions 💖

• --allJunctions — Detect exon-exon junctions (both canonical and non-canonical junctions) and structural variants in RNA-seq data. Refer to the Users Guide for reporting of junctions and fusions. ✨

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🌸 gene annotation 🌸

• -a — Name of an annotation file (a gzipped file is accepted). GTF/GFF format by default. See the -F option for more format information.
• -F — Specify the format of the provided annotation file. Acceptable formats include 'GTF' (or compatible GFF format) and 'SAF'. 'GTF' by default. For SAF format, please refer to the Users Guide.
• -A — Provide a chromosome name alias file to match chr names in the annotation with those in the reads. This should be a two-column comma-delimited text file. Its first column should include chr names in the annotation and its second column should include chr names in the index. Chr names are case sensitive. And no column header should be included in the file, okay? None. 🙅
• --gtfFeature <string> — Specify feature type in GTF annotation. 'exon' by default. Features used for read counting will be extracted from the annotation using the provided value.
• --gtfAttr <string> — Specify attribute type in GTF annotation. 'gene_id' by default. Meta-features used for read counting will be extracted from the annotation using the provided value.

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⭐ others ⭐

• -v — Output version of the program.

Refer to the Users Manual for a detailed description of the arguments. 📖

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👑 AUTHOR 👑

This manpage was written by Alexandre Mestiashvili for the Debian distribution, and can be used for any other usage of the program. Slay, honestly. 🫶

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okay bestie that's the whole page, we did it 💅✨ — and just so you know where all this came from: it's subjunc 2.0.3, dated March 2023, straight outta SUBJUNC(1). mwah 🎀