Usage

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This page will teach you how to:

• Run slncky
• Customize slncky
• Understand slncky's output

Run slncky !

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Usage: ./slncky.v1.0 bedfile assembly out_prefix

Customize slncky
General Options
-c / --config	Specify path of annotations.config file. (Default:annotations.config assumed to be in same directory as ./slncky executable.)
-1 / --no_orth_search	Only filter; don't search for orthologs.
-2 / --no_filter	Don't filter; only search for orthologs.
-o / --overwrite	Force overwrite of trancsripts.lncs.bed.
-n / --threads	Number of threads to use for aligning transcripts. (Default: 5)
-w / --web	Create browser to visualize aligned lncRNAs.
--bedtools	Path to bedtools executables. (Default: bedtools assumed to be in user's PATH)
--liftover	Path to liftover executable. (Default: bedtools assumed to be in user's PATH)
--lastz	Path to lastz executable. (Default: bedtools assumed to be in user's PATH)
Filter Options
--min_overlap	Minimum overlap for filtering transcripts overlapping CODING or MAPPED_CODING gene. (Default: 0.00)
--min_cluster	Minimum size of duplication cluster for filtering paralogous transcripts. (Default: 2)
--min_coding	Minimum identity for filtering transcripts that align to syntenic CODING gene. (Default: slncky learns threshold from input data.)
--no_collapse	Do not collapse overlapping transcripts into single canonical gene.
--no_overlap	Do not remove transcripts that overlap CODING or MAPPED_CODING gene.
--no_self	Do not remove transcripts sharing sequence similarity with each other.
--no_dup	Do not remove transcripts that share sequence similarity with DUP genes.
--no_coding	Do not remove transcripts that align to syntenic CODING genes.
Orthology Search Options
--min_noncoding	Minimum overlap for reporting transcripts that align to syntenic NONCODING gene. (Default: slncky learns threshold by aligning to shuffled intergenic regions)
--no_bg	Do not align to shuffled background; report all alignments. Setting this option will greatly reduce slncky runtime.
--no_orf	Do not check for conserved ORFs in aligned noncoding transcripts.
Advanced orthology search options
--minMatch	minMatch parameter to pass to liftOver. Decreasing this parameter will increase sensitivity of orthology search. (Default: 0.1)
--pad	Number of basepairs up- and downstream of lncRNA loci to include in orthology search. Increasing this parameter will increase sensitivity of orthology search. (Default: 50,000)
--gap_open	Gap open penalty to pass to lastz. Decreasing this parameter will increase sensitivity of orthology search. (Default: 1.0)
--gap_extend	Gap extend penalty to pass to lastz. Decreasing this parameter will increase sensitivity of orthology search. (Default: 40)

Output

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out.lncs.bed
Bed12 file of high-confidence long, non-coding RNAs

out.lncs.info.txt
A table of final lncRNA transcripts, names, category, based on supplied annotations.

out.filtered_info.txt / out.cluster_info.txt
filter_info contains a list of every filtered out transcripts with the reason for filtering. cluster_info contains names of transcripts found in duplication clusters

out.canonical_to_lncs.txt
A table of the canonical transcripts chosen from groups over overlapping transcripts.

out.orthologs.txt / out.orthologs.top.txt
A list of every ortholog pair, with additional information about the alignment. The out.orthologs.top.txt file contains only the best alignment (based on exonic identity) for each lncRNA.

out.orfs.txt
A list of alignments which contain ORFs longer than 30bp, along with additional information about the ORF alignment.

out_browser/
If the --web flag was set, slncky will create an evolutionary browser that is viewable from out_browser/browse.html