Fastq mcf - Revision history

Sspintus@dote.ru at 10:35, 25 March 2019

2019-03-25T10:35:05Z

Sspintus@dote.ru at 10:33, 25 March 2019

2019-03-25T10:33:53Z

Sspintus@dote.ru at 10:31, 25 March 2019

2019-03-25T10:31:51Z

Sspintus@dote.ru at 10:31, 25 March 2019

2019-03-25T10:31:10Z

Sspintus@dote.ru at 10:29, 25 March 2019

2019-03-25T10:29:47Z

Sspintus@dote.ru at 10:28, 25 March 2019

2019-03-25T10:28:30Z

Sspintus@dote.ru: /* Introduction */

2019-03-25T10:23:11Z

‎Introduction

Sspintus@dote.ru at 10:19, 25 March 2019

2019-03-25T10:19:56Z

Sspintus@dote.ru at 10:19, 25 March 2019

2019-03-25T10:19:33Z

Sspintus@dote.ru at 10:17, 25 March 2019

2019-03-25T10:17:44Z

← Older revision		Revision as of 10:35, 25 March 2019
Line 85:		Line 85:

	Quality filters are evaluated after clipping/trimming		Quality filters are evaluated after clipping/trimming
		+
		+	==Links==

	[https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMcf.md fastq-mcf on GitHub]		[https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMcf.md fastq-mcf on GitHub]

@@ Line 25: / Line 25: @@
 required for each.  IE: -o read1.clip.q -o read2.clip.fq
-====Options:====
+====Options====
      -h       This help
      -o FIL   Output file (stats to stdout)
@@ Line 49: / Line 49: @@
      -d       Output lots of random debugging stuff
-====Quality adjustment options:====
+====Quality adjustment options====
      --cycle-adjust    CYC,AMT     Adjust cycle CYC (negative = offset from end) by amount AMT
      --phred-adjust    SCORE,AMT   Adjust score SCORE by amount AMT
-====Filtering options:====
+====Filtering options====
      --[mate-]qual-mean  NUM       Minimum mean quality score
      --[mate-]qual-gt    NUM,THR   At least NUM quals > THR
@@ Line 85: / Line 85: @@
 Quality filters are evaluated after clipping/trimming

@@ Line 25: / Line 25: @@
 required for each.  IE: -o read1.clip.q -o read2.clip.fq
-===Options:===
+====Options:====
      -h       This help
      -o FIL   Output file (stats to stdout)
@@ Line 49: / Line 49: @@
      -d       Output lots of random debugging stuff
-===Quality adjustment options:===
+====Quality adjustment options:====
      --cycle-adjust    CYC,AMT     Adjust cycle CYC (negative = offset from end) by amount AMT
      --phred-adjust    SCORE,AMT   Adjust score SCORE by amount AMT
-===Filtering options:===
+====Filtering options:====
      --[mate-]qual-mean  NUM       Minimum mean quality score
      --[mate-]qual-gt    NUM,THR   At least NUM quals > THR

@@ Line 13: / Line 13: @@
 <code>
 Usage: fastq-mcf [options] <adapters.fa> <reads.fq> [mates1.fq ...]<br>
 </code>
 Detects levels of adapter presence, computes likelihoods and
@@ Line 21: / Line 20: @@
 Stats go to stderr, unless <code>-o</code> is specified.
-Specify -0 to turn off all default settings
+Specify <code>-0</code> to turn off all default settings
 If you specify multiple 'paired-end' inputs, then a -o option is
 required for each.  IE: -o read1.clip.q -o read2.clip.fq
-Options:
+===Options:===
      -h       This help
      -o FIL   Output file (stats to stdout)
@@ Line 50: / Line 49: @@
      -d       Output lots of random debugging stuff
-Quality adjustment options:
+===Quality adjustment options:===
      --cycle-adjust    CYC,AMT     Adjust cycle CYC (negative = offset from end) by amount AMT
      --phred-adjust    SCORE,AMT   Adjust score SCORE by amount AMT
-Filtering options*:
+===Filtering options:===
      --[mate-]qual-mean  NUM       Minimum mean quality score
      --[mate-]qual-gt    NUM,THR   At least NUM quals > THR

@@ Line 12: / Line 12: @@
 ==Usage==
 <code>
-Usage: fastq-mcf [options] <adapters.fa> <reads.fq> [mates1.fq ...]
+Usage: fastq-mcf [options] <adapters.fa> <reads.fq> [mates1.fq ...]<br>
-Version: 1.04.636
+Version: 1.04.636<br>
 </code>
 Detects levels of adapter presence, computes likelihoods and

← Older revision		Revision as of 10:23, 25 March 2019
Line 9:		Line 9:
	* Discard sequences that are too short after all of the above		* Discard sequences that are too short after all of the above
	* Keep multiple mate-reads in sync while doing all of the above		* Keep multiple mate-reads in sync while doing all of the above
		+
		+	==Usage==
		+	<code>
		+	Usage: fastq-mcf [options] <adapters.fa> <reads.fq> [mates1.fq ...]
		+	Version: 1.04.636
		+
		+	Detects levels of adapter presence, computes likelihoods and
		+	locations (start, end) of the adapters. Removes the adapter
		+	sequences from the fastq file(s).
		+
		+	Stats go to stderr, unless -o is specified.
		+
		+	Specify -0 to turn off all default settings
		+
		+	If you specify multiple 'paired-end' inputs, then a -o option is
		+	required for each. IE: -o read1.clip.q -o read2.clip.fq
		+
		+	Options:
		+	-h This help
		+	-o FIL Output file (stats to stdout)
		+	-s N.N Log scale for adapter minimum-length-match (2.2)
		+	-t N % occurance threshold before adapter clipping (0.25)
		+	-m N Minimum clip length, overrides scaled auto (1)
		+	-p N Maximum adapter difference percentage (10)
		+	-l N Minimum remaining sequence length (19)
		+	-L N Maximum remaining sequence length (none)
		+	-D N Remove duplicate reads : Read_1 has an identical N bases (0)
		+	-k N sKew percentage-less-than causing cycle removal (2)
		+	-x N 'N' (Bad read) percentage causing cycle removal (20)
		+	-q N quality threshold causing base removal (10)
		+	-w N window-size for quality trimming (1)
		+	-H remove >95% homopolymer reads (no)
		+	-0 Set all default parameters to zero/do nothing
		+	-U\|u Force disable/enable Illumina PF filtering (auto)
		+	-P N Phred-scale (auto)
		+	-R Dont remove Ns from the fronts/ends of reads
		+	-n Dont clip, just output what would be done
		+	-C N Number of reads to use for subsampling (300k)
		+	-S Save all discarded reads to '.skip' files
		+	-d Output lots of random debugging stuff
		+
		+	Quality adjustment options:
		+	--cycle-adjust CYC,AMT Adjust cycle CYC (negative = offset from end) by amount AMT
		+	--phred-adjust SCORE,AMT Adjust score SCORE by amount AMT
		+
		+	Filtering options*:
		+	--[mate-]qual-mean NUM Minimum mean quality score
		+	--[mate-]qual-gt NUM,THR At least NUM quals > THR
		+	--[mate-]max-ns NUM Maxmium N-calls in a read (can be a %)
		+	--[mate-]min-len NUM Minimum remaining length (same as -l)
		+	--hompolymer-pct PCT Homopolymer filter percent (95)
		+
		+	If mate- prefix is used, then applies to second non-barcode read only
		+
		+	Adapter files are 'fasta' formatted:
		+
		+	Specify n/a to turn off adapter clipping, and just use filters
		+
		+	Increasing the scale makes recognition-lengths longer, a scale
		+	of 100 will force full-length recognition of adapters.
		+
		+	Adapter sequences with _5p in their label will match 'end's,
		+	and sequences with _3p in their label will match 'start's,
		+	otherwise the 'end' is auto-determined.
		+
		+	Skew is when one cycle is poor, 'skewed' toward a particular base.
		+	If any nucleotide is less than the skew percentage, then the
		+	whole cycle is removed. Disable for methyl-seq, etc.
		+
		+	Set the skew (-k) or N-pct (-x) to 0 to turn it off (should be done
		+	for miRNA, amplicon and other low-complexity situations!)
		+
		+	Duplicate read filtering is appropriate for assembly tasks, and
		+	never when read length < expected coverage. -D 50 will use
		+	4.5GB RAM on 100m DNA reads - be careful. Great for RNA assembly.
		+
		+	Quality filters are evaluated after clipping/trimming
		+	</code>

← Older revision		Revision as of 10:19, 25 March 2019
Line 1:		Line 1:
−	=Introduction=	+	==Introduction==

	fastq-mcf attempts to:		fastq-mcf attempts to:

@@ Line 2: / Line 2: @@
 fastq-mcf attempts to:
-  *Detect & remove sequencing adapters and primers
+* Detect & remove sequencing adapters and primers
-  *Detect limited skewing at the ends of reads and clip
+* Detect limited skewing at the ends of reads and clip
-  *Detect poor quality at the ends of reads and clip
+* Detect poor quality at the ends of reads and clip
-  *Detect Ns, and remove from ends
+* Detect Ns, and remove from ends
-  *Remove reads with CASAVA 'Y' flag (purity filtering)
+* Remove reads with CASAVA 'Y' flag (purity filtering)
-  *Discard sequences that are too short after all of the above
+* Discard sequences that are too short after all of the above
-  *Keep multiple mate-reads in sync while doing all of the above
+* Keep multiple mate-reads in sync while doing all of the above