This option is primarily useful in ATACseq experiments, for filtering mono- or di-nucleosome fragments. The minimum fragment length needed for read/pair inclusion. For example, to get only reads that map to the forward strand, use –samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand. (Default: None)Įxclude reads based on the SAM flag. This is useful to count properly paired reads only once, as otherwise the second mate will be also considered for the coverage. For example, to get only reads that are the first mate, use a flag of 64. This option is useful to get a sharper signal around enriched regions. For single-end data, the given fragment length is used. For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. If set, only reads that have a mapping quality score of at least this are considered.īy adding this option, reads are centered with respect to the fragment length. If reads are paired, the mate’s position also has to coincide to ignore a read. If set, reads that have the same orientation and start position will be considered only once. If no value is specified, it is estimated from the data (mean of the fragment size of all mate reads). The input of a fragment length value is optional. Unmated reads, mate reads that map too far apart (>4x fragment length) or even map to different chromosomes are treated like single-end reads. Paired-end: Reads with mates are always extended to match the fragment size defined by the two read mates. Reads that already exceed this fragment length will not be extended. Single-end: Requires a user specified value for the final fragment length. NOTE: This feature is generally NOT recommended for spliced-read data, such as RNA-seq, as it would extend reads over skipped regions. If set, each read is extended, without exception. This parameter allows the extension of reads to fragment size.
Blue fingerprint stock photo 111382244.Read processing options ¶ -extendReads, -e
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