Version 0.0
Peak-calling for genomic enrichment assays of treatment sample(s) (-t [<file>]+
), with or without control sample(s) (-c [<file>]+
). Input files must be in SAM/BAM format. Incorporates ideas from SAMtoBED
, removeChrom
, and MACS2 v2.1.2_dev
.
- Control of analysis of alignments:
- Properly paired alignments only (default); fragments are inferred appropriately
- Also keeping unpaired alignments:
- As they appear in the SAM/BAM file (
-y
) - Length increased to specified value (
-a <int>
) - Length increased to average value of paired alignments (
-x
)
- As they appear in the SAM/BAM file (
- Filtering options:
- Chromosomes (reference sequences) to ignore (
-e <arg>
) - Minimum mapping quality (
-m <int>
)
- Chromosomes (reference sequences) to ignore (
- Peak-calling options:
- Maximum q-value (
-q <float>
, def. 0.05) - Maximum p-value (
-p <float>
) - Minimum length of a peak (
-l <int>
, def. 100bp) - Maximum distance between significant sites (
-g <int>
, def. 100bp)
- Maximum q-value (
- Output options:
- Output peak file, in ENCODE narrowPeak format (
-o <file
) - Output bedgraph file listing treatment/control pileups and p/q values (
-b <file>
)
- Output peak file, in ENCODE narrowPeak format (