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Description

This tool recursively align sequenced files to any number of index files in given order. When the sequenceces are aligned to an index file, the rest of the sequences are going to align to the next index file. For each alignment, the pipeline produces a stats file, an alignment file, quant file for each fasta sequence of given index file and the rest of the data.

Input Dir: Full path of the input directory that includes the libraries.
Input Params: Input files are given in two or three columns for the libraries. If the files are paired end enter three columns. First column is the name of the library, second column is the location of the first pair and third is the the second pair. If there is single end libraries, use two columns. The name of the library and the location of the file in the cluster. You can use 'DIR' keyword to denote 'Input Dir' to prevent repetition of entering full path for each libraries. If you give the same name for more than one library, the pipeline will merge them.
Index File Full Path: This is the index file that is prepared using bowtie-build. It requires the fullpath and the name of the index file. without extensions.
Name of the step: The name of the index file. This name will be used generated outputs. Ex:outdir/libname.indexname.stats
Bowtie Parameters: Bowtie parameters for this individual step.
Description: This is the description of the step. This naming will be used to produce summary file and calculation of the total counts to mapped to this step.
Filter Out: To filter out the reads and move on to next step. This should be selected yes. If it is no, the sequences will be used without filtered out in the next step. So, if this step selected no, there can be overcount in summary tables.