Track statistics (analysis)

Analysis title

Track statistics

Provider

Institute of Systems Biology

Class

SequenceStatistics

Plugin

ru.biosoft.bsastats (Bio-sequences analyses plugin extension)

Description

Gather various statistics about track or FASTQ file.

Parameters:

• Source – Whether to get input data from track or from FASTQ
• Input track – Track to process
• FASTQ file – FASTQ file with reads to analyze
• Quality encoding – This specifies how phred quality values are encoded in the FASTQ file. In most of the cases system detects this value automatically. You may change it manually if auto-detection worked incorrectly.
• CSFasta file – File containing reads in color space
• Qual file – File containing corresponding quality values
• Alignment – Whether to align sites on left or right
• Processors – List of methods to gather the statistics
  • Basic statistics – Gathers basic statistics like reads count and average read length
  • Quality per base – Distribution of phred quality score along the bases
  • Quality per sequence – Distribution of phred quality score among the sequences
  • Nucleotide content per base – Distribution of individual nucleotides along the bases
  • GC content per base – Distribution of GC along the bases
  • GC content per sequence – Draws a distribution of GC content among reads
  • N content per base – Distribution of 'N' along the bases
  • Sequence length distribution – Calculates distribution of read lengths and outputs them as the table and as the chart
  • Duplicate sequences – Calculate the rate of sequences duplication: how many sequences occurs 2, 3 and so on times relative to unique sequences. This statistic is based on the first 200000 reads
  • Overrepresented sequences – Look for sequences which appear in more than 0.1% cases
  • Overrepresented K-mers – Search for K-mers which are represented 3x times per sequence or 5x times per position
  • Overrepresented prefixes – Search for read prefixes (starting from the read start) up to 15 bp long which are overrepresented in the set.
• Output path – Path to the output folder (will be created)