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By Aronesty E., Last update 1494698998
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sam-stats description

Sam-stats computes statistics from (possibly compressed) SAM or BAM files. Some of the output statististics: mapped reads - if duplicate tracking was enabled via -D, it recapitulates the number of unique, mapped, probe-id*s in the original sam file. It is multiplied by 2 for paired-end data with duplicate read id*s. If you divide this by the number of reads in the fastq you aligned (possibly from the output of fastq-stats), you will get an accurate 'percentage of reads aligned' statistic. Pct ambiguous - 100 divided by where 'aligning more than once' means more than 2 alignments for paired end and more than 1 alignment for single-end. max dup align - The maximum number of alignments for a single probe-id. IE: if seq4455 aligns 50 times, and this is more than any other sequence, then the result would be 50. For paired-end reads one is subtracted, since you should get two alignments with the same probe-id for each read, but anything more than that is considered 'ambiguous'. singleton mappings - number of reads that aligned only once. total mappings - the number of lines in the sam file that were 'mapped' reads. For a complete list of statistics check https: or or code.google.com or p or ea-utils or wiki or SamStatsDetails

Parent program: ea-utils

Ea-utils is FASTQ processing utilities such as fastq-mcf, fastq-multx, fastq-join, varcall and sam-stats and other. These tools detect and remove sequencing adapters and primers, detect limited skewing at the ends of reads and clip, poor quality at the ends of reads and clip, discard sequences that are too short after all of the above, keep multiple mate-reads in sync while doing all of the above, merge overlapping paired-end reads and computing statisticsfrom SAM, BAM or Fasta files.