Miscellaneous tools

Below are listed other miscellaneous programs that we’ve released at one time or another. Many of these have all been supplanted with better implementations (either in the latest ShortStack release or the latest CleaveLand4 release)… but in case they are needed they are provided here or on github:

From github.com/MikeAxtell

  • bam2wig : Conversion of a BAM alignment to wiggle and bigwig coverage files, with flexible reporting options. (no longer included as part of ShortStack but we still use this one for making good bigwig browser tracks from small RNA bam files)
  • butter : Bowtie UTilizing iTerative placEment of Repetitive small rnas. (Deprecated as ShortStack 3.x and higher contain similar alignment functions)
  • maple : MicroRNA Analysis Program Leveraging Expression (Deprecated as ShortStack 3.x and higher contain similar microRNA analysis functions)
  • sim_srna-seq : Simulation of plant small RNA-seq data (Deprecated)
  • GSTAr :  GSTAr: Generic Small RNA-Transcriptome Aligner (not really deprecated .. it is also a component of CleaveLand4)

Other old scripts

The functionalities of most of these perl scripts are now provided in ShortStack versions 3.x and higher. The major exception is find_3p_adapter , which we still find quite useful for determining the 3′ adapter sequenced used in a given small RNA-seq library.

  • trim_SOLiD_sRNA_cs-fastq.pl  :: Trim 3′ adapters off the ends of colorspace small RNA reads provided in cs-fastq format

  • trim_SOLiD_sRNA_cs-fasta.pl :: Trim 3′ adapters off the ends of colorspace small RNA reads provided in csfasta format.  Basically the same program as version 2.2 of the above, except modified to take in .csfasta instead of .cs-fastq formatted data.

  • csfasta2cs-fastq.pl :: combine native .csfasta and .qual files produced by the SOLiD instrument into a single .cs-fastq formatted file

  • trim_illumina_sRNA_fastq.pl  :: Trim 3′ adapters off the ends of fastq-formatted small RNA reads

  • find_3p_adapter :: Using a known, abundant microRNA sequence, infer the 3′ adapter sequence from a fastq-formatted small RNA library