Revision as of 09:57, 5 October 2016 (view source) Czhang (Talk | contribs) ← Older edit		Latest revision as of 16:11, 15 November 2016 (view source) Czhang (Talk | contribs) (→‎tag2peak.pl)
Line 462:		Line 462:
	| --out-half-PH [string]		| --out-half-PH [string]
	| output half peak height boundaries		| output half peak height boundaries
		+	|-
		+	| --dbkey [string]
		+	| species to retrieve the default gene bed file
	|-		|-
	| --gene [string]		| --gene [string]
−	| gene bed file for scan statistics	+	| custom gene bed file for scan statistics (will override --dbkey)
	|-		|-
	| --use-expr		| --use-expr

---

Latest revision as of 16:11, 15 November 2016

fastq_filter.pl

Usage: fastq_filter.pl [options] <in.fq> <output.fq (or out.fa)>

Arguments:

Argument	Description
<in.fq>	input file in FASTQ format
<out.fq (or out.fa)>	output file of filtered FASTQ format

Options:

Option	Description
-v	verbose
-if [string]	fastq format (solexa or [sanger])
-index [string]	index position and sequence (e.g. 0:CAGT)
-f [string]	quality score filter string (method1:start1-end1:score1,method2:start2-end2:score2, zero-based)
-maxN [int]	max number of N in sequence (default off)
-of [string]	output format (fasta or [fastq])

fastq2collapse.pl

Usage: fastq2collapse.pl [options] <in.fq> <out.fq>

Arguments:

Argument	Description
<in.fq>	input file in FASTQ format of filtered and trimmed reads
<out.fq>	output file in FASTQ format in which exact PCR duplicates have been collapsed

Options:

Option	Description
--tmp-dir [string]	temporary directory
-v	verbose

stripBarcode.pl

Usage: stripBarcode.pl [options] <in.fastq> <out.fastq>

Arguments:

Argument	Description
<in.fastq>	input file in FASTQ format that contains 5' linker degenerate barcodes
<out.fastq>	output file in FASTQ format with barcodes removed and attached to sequence ids

Options:

Option	Description
-len [int]	length of barcode sequences
-format [string]	input format ([fasta] or fastq)
--barcode-start-with [string]	filter sequences based on the starting nucleotides in the barcode
--barcode-end-with [string]	filter sequences based on the ending nucleotides in the barcode
--tmp-dir [string]	temporary directory
--keep-cache	keep cache when the job is done
-v	verbose

parseAlignment.pl

Usage: parseAlignment.pl [options] <in.sam> <tag.bed>

Arguments:

Argument	Description
<in.sam>	input file in SAM format after alignment/mapping
<tag.bed>	parsed output file in BED format of tag alignment

Options:

Option	Description
--mutation-file [string]	file name to save mutations
--map-qual [int]	MAPQ score (e.g. to keep only uniquely mapped reads)
--min-len [int]	minimal read length to report
--indel-to-end [int]	nucleotides from indel to end
--split-del	split oligo deletion into single nucleotides
--indel-in-score	count indels in as mismatches reported in the score column
-v	verbose

tag2collapse.pl

See more information about model in:

Darnell JC, et al. FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism. Cell. 2011; 146:247–261

Usage: tag2collapse.pl [options] <tag.bed> <tag.uniq.bed>

Arguments:

Argument	Description
<tag.bed>	input file in BED format of CLIP tags
<tag.uniq.bed>	output file in BED format of unique CLIP tags

Options:

Option	Description
Input options
-big	set when the input file is big
-weight	consider the weight of each tag
--weight-in-name	find weight in name
EM options
--random-barcode	random barcode exists, no collapse for different barcodes
-EM [int]	EM threshold to infer reliability of each collapsed read (when have random linker, -1=no EM)
--seq-error-model [string]	sequencing error model to use (alignment or [em-local] or em-global or fix=0.01)
--output-seq-error [file]	output sequencing errors estimated by the EM algorithm
Output options
--keep-max-score	keep the tag with the most weight (instead of the longest one) as representative
--keep-tag-name	do not change tag name (no extra information)
Other options
-c [string]	cache directory
--keep-cache	keep cache when the job is done
-d	debug (on or [off])
-v	verbose

selectRow.pl

Usage: selectRow.pl [options] <mutation.txt> <tag.uniq.bed> > <tag.uniq.mutation.txt>

Arguments:

Argument	Description
<mutation.txt>	input file in txt format of mutations from alignment parsing
<tag.uniq.bed>	input file in BED format of unique CLIP tags
<tag.uniq.mutation.txt>	output file in txt format of unique mutations

Options:

Option	Description
-h	the file has a header to be included
-q [int]	query column id (zero-based) (default=0)
-f [int]	filter column id (zero-based) (default=0)
-i	ignore case (default=off)
-p	print the key without matches (default=off)
-pt	the text to print when no match exist (No match found)
-s	print in single line if there are multiple matches (default=off)
-d	delimiter when -s is specified
-ss	print only one match if there are multiple matches (default=off)

bed2rgb.pl

Usage: bed2rgb.pl [options] <tag.uniq.bed> <tag.uniq.rgb.bed>

Arguments:

Argument	Description
<tag.uniq.bed>	input file in BED format of unique CLIP tags
<tag.uniq.rgb.bed>	output file in BED format of rgb colored unique CLIP tags

Options:

Option	Description
-col [string]	color by name or rgb (blue or red or green...r,g,b)
-v	verbose

bed2annotation.pl

Usage: bed2annotation.pl [options] <tag.uniq.annot.summary.txt (optional)><tag.uniq.rgb.bed (or tag.uniq.bed)> <tag.uniq.annot.txt>

Arguments:

Argument	Description
<tag.uniq.annot.summary.txt> (optional)	output file in txt format of a summary of the annotation if -summary option is used
<tag.uniq.rgb.bed (or tag.uniq.bed)>	input file in BED format of unique CLIP tags (with or without rgb color)
<tag.uniq.annot.txt>	output file in txt format of annotation

Options:

Option	Description
-conf [file]	configuration file with input datasets
-dbkey [string]	genome build name (hg19 or mm10)
-ss	consider the two strands separately when possible
-big	big file
-gene	annotate overlapping gene (id and symbol)
-rmsk	annotate overlapping RepeatMasked sequences (type and %)
-miRNA	annotate miRNA (miRNA_name)
-region	annotate genomic breakdown
-custom [file]	annotate custom features in the provided BED file
--custom-name [string]	naming the custom feature
--custom-summary [string]	method to summarize custom annotation ([all]or max_num or min_num or max_overlap)
-summary [file]	print summary information
-c [string]	cache directory
--keep-cache	keep cache when the job is done
-v	verbose

tag2peak.pl

Usage: tag2peak.pl [options] <tag.uniq.bed> <peak.bed>

Arguments:

Argument	Description
<tag.uniq.bed> (with or without rgb)	input file in BED format of unique CLIP tags
<peak.bed>	output file in BED format of peaks called
Optional arguments
<tag.uniq.peak.boundary.bed>	output file in BED format of cluster boundaries (if --out-boundary option used)
<tag.uniq.peak.halfPH.bed>	output file in BED format of half peak height boundaries (if --out-half-PH used)

Options:

Option	Description
-big	big input file
-ss	separate the two strands
--valley-seeking	find candidate peaks by valley seeking
--valley-depth [float]	depth of valley if valley seeking (between 0.5 and 1, default=0.9)
--out-boundary [string]	output cluster boundaries
--out-half-PH [string]	output half peak height boundaries
--dbkey [string]	species to retrieve the default gene bed file
--gene [string]	custom gene bed file for scan statistics (will override --dbkey)
--use-expr	use expression levels given in the score column in the gene bed file for normalization
-p [float]	threshold of p-value to call peak (e.g. 0.01)
--multi-test	do Bonferroni multiple test correction
-minPH [int]	min peak height
-maxPH [int]	max peak height
-gap [int]	merge cluster peaks closer than the gap (-1, no merge if < 0)
--prefix [string]	prefix of peak id (Peak) (so output file will look like Peak1, Peak2, etc)
-c [dir]	cache dir
--keep-cache	keep cache when the job done
-v	verbose

tag2profile.pl

Usage: tag2profile.pl [options] <tag.uniq.bed> <peak.sig.boundary.count.bed> 

Arguments:

Argument	Description
<tag.uniq.bed>	input file in BED format of unique CLIP tags (with or without rgb color)
<peak.sig.boundary.count.bed>	output file in BED format of peak profile
<peak2.sig.boundary.count.bed> (Optional argument)	for wig format output, specify two files to separate the two strands

Options:

Option	Description
Input options
-big	big file
-minBlockSize [int]	minimum number of lines to read in each block for a big file
-weight	weight counts according to the score of each tag
-weight-avg	weight average the score of each tag
-ss	separate strand
-ext5 [int]	extension of tags at the 5' end
-ext3 [int]	extension of tags at the 3' end
-chrLen [string]	chrom length file
Profile options
-region [file]	a bed file with regions to count tag numbers. If not specified, count in moving windows
-exact	exact count at each nucleotide
-w [int]	window size
-s [int]	step size
--normalize [string]	normalization ([none] or rpkm or multiply={1.3})
Output options
-of [string]	output format ([bed] or bedgraph or sgr)
-nz	don't print zeroes (works for sgr and bed)
-n [string]	track name
-c [string]	cache directory
--keep-cache	keep cache when the job is done
-v	verbose

CIMS.pl

Usage: CIMS.pl [options] <tag.uniq.bed> <CIMS.mutation.bed> <CIMS.mutation.txt>

Arguments:

Argument	Description
<tag.uniq.bed>	input file in BED format of unique CLIP tags (with or without rgb)
<CIMS.mutation.bed>	output file in BED format of deletions, insertions, or substitutions (CIMS)
<CIMS.mutation.txt>	output file in txt format of CIMS

Options:

Option	Description
-big	big file
-w [int]	mutation size
-n [int]	number of iterations for permutation
-p	track mutation position relative to read start
--no-sparse-correct	no sparcity correction
-FDR [float]	threshold of FDR
-mkr [float]	threshold of m-over-k-ratio
-c [dir]	cache directory
--keep-cache	keep cache when the job is done
-v	verbose

removeRow.pl

Usage: removeRow.pl [options] <tag.uniq.bed> <mutation.bed> > <tag.uniq.clean.bed>

Arguments:

Argument	Description
<tag.uniq.bed>	input file in BED format of unique CLIP tags
<mutation.bed>	input file in BED format of CIMS
<tag.uniq.clean.bed>	output file in BED format in which CLIP tags with deletions are removed

Options:

Option	Description
-q [int]	query column id (zero-based) (default=0)
-f [int]	filter column id (zero-based) (default=0)
-i	ignore case (default=off)
-r	reverse mode
-v	verbose

bedExt.pl

Usage: bedExt.pl [options] <tag.uniq.clean.bed> <tag.uniq.clean.trunc.bed>

Arguments:

Argument	Description
<tag.uniq.clean.bed>	input file in BED format in which CLIP tags with deletions were removed
<tag.uniq.clean.trunc.bed>	output file in BED format extended around start site as a potential cross link site that causes truncation

Options:

Option	Description
-n	get neighbor region relative to <up or down or r=100>
-l	extension on the left
-r	extension on the right
-chrLen [string]	chromosome length file
-v	verbose

tag2cluster.pl

Usage: tag2cluster.pl [options] <tag.uniq.bed> <cluster.bed>

Arguments:

Argument	Description
<tag.uniq.bed>	input file in BED format of unique CLIP tags
<cluster.bed>	output file in BED format of clustered overlapping CLIP tags

Options:

Option	Description
-big	big file
-s	same strand required
-weight	consider the weight of each tag
--weight-in-name	find weight in name
-maxgap [int]	the max gap to be considered as an overlap
-collapse [int]	collapse mode (0: no collapse; 1: collapse if match both ends; 2: collapse if one is in another)
-overlap [float]	overlap fraction, effective unless collapse
-of [string]	output format ([bed] or wig)
-c [string]	cache directory
--keep-cache	keep cache when the job is done
-d	debug (on or [off])
-v	verbose