![]() minr minimum pearson correlation to calculate shift (0.5) chrom number of chromosomes to sample (4) H -shiftval explicit shift value in bp (default is to calculate) x -extval explicit extension size in bp (default is to calculate) I -shift shift reads in the 3' direction intron maximum allowed gap (intron) size in bp (none) U -nosupplementary ignore supplementary (0x800) alignments (false) D -noduplicate ignore duplicate (0x400) alignments (false) S -nosecondary ignore secondary (0x100) alignments (false) B -blacklist interval file of regions to skip (bed, gff, txt) K -chrskip regular expression to skip chromosomes second only process paired second read (0x80) as single-end first only process paired first read (0x40) as single-end maxsize maximum allowed insertion size (600) minsize minimum allowed insertion size (30) P -fastpe process paired-end alignments, only F are checked p -pe process paired-end alignments, both are checked t -strand record separate strands as two wig files smartcov record paired coverage without overlaps, splices cspan record a span centered on midpoint ![]() ![]() e -extend extend alignment (record predicted fragment) a -span record across entire alignment or pair d -mid record at midpoint of alignment or pair i -in repeat if multiple bams, or comma-delimited list SYNOPSISī -extend -rpm -mean -out file -bw file1.bam file2.bam Required options: TEXT REPRESENTATION OF RECORDING ALIGNMENTSĪ program to convert Bam alignments into a wig representation file. ![]()
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