Hit2Wiggle.pl - Clusters reads using a sliding window approach into the wiggle format
# Minimal argument call specifying all required parameters.
Hit2Wiggle.pl --input Mapping_day0_1_i_Eland_against_mature_unambiguous.txt
--output day0.wig
# Maximum argument call specifying all possible parameters; Several different input files may be specified
# Note that also the file containing the ambiguous hits may be specified
Hit2Wiggle.pl --output day0.wig --min_length 15 --max_length 32 --max_mm 2 --strand RF
--min_count 10 --max_ambiguity 2 --tempdir "/tmp"
--window_size 1000
--input Mapping_day0_1_i_Eland_against_mature_unambiguous.txt
--input Mapping_day0_1_i_Eland_against_mature_ambiguous.txt
The input files; Several files may be specified, e.g.: --input file1 --input file2.
The input files have to be output files of the script run_Mapping or run_Multimapper.
Note that unambiguously and ambiguously mapped reads may be provided for this script. Mandatory parameter.
The output file. Mandatory parameter
Only reads mapping to the specified strand will be used. You may also specify both strands in which case reads from different strands will be clustered in the same window!! Possible values: R (reverse strand), F (forward strand), RF (both strands); default=RF
The minimum length of reads. Shorter reads will be ignored. default=15
The maximum length of reads. Longer reads will be ignored. default=100
The maximum number of mismatches. Reads having more mismatches will not be used. default=2
The maximum ambiguity of the hits. Hits having a higher ambiguity will be ignored. The ambiguity is an integer value which relates how often a read could be mapped with an equal good score (number of mismatches) to the reference sequence. Examples:
A read which could be mapped to the H. sapiens genome only once having two mismatches, will have a ambiguity of "1".
A read which could be mapped to the H. sapiens genome three times, always having one mismatch, will have a ambiguity of "3".
A read which could be mapped to the H. sapiens genome three times having one mismatch and one time having zero mismatches, will have a ambiguity of "1".
A read which could be mapped to the H. sapiens genome three times having one mismatch and two times having zero mismatches, will have a ambiguity of "2".
default=5
Minimum counts for a wiggle window. Windows having less reads will not be reported. default=1
The size of the sliding window; default=1000
The name of the track. This information may for example be displayed in the genome browser. default=unknown
The temporary directory used; default=/tmp
Display the help pages.
The script clusters hits using a sliding window approach into the wiggle format. The wiggle format is supported by most genome browsers.
Mapping results of the script run_Mapping.pl or run_Multimapper.pl.
Note that unambiguous and ambiguous mapping results may be provided.
For example:
5031||Count=1 TCCCCGCCGGCGGAA chr4 1 0 F 170168086 5217||Count=1 GACCGTCCAACGCAC chr20 1 0 R 59264663 5560||Count=1 ATCGGGTGGTAGCAA chr3 1 0 F 16192245 6184||Count=1 TCCGGGCTACTGCTG chr1 1 0 F 29388851 6209||Count=1 GCAGCCATCGTTTTT chr10 1 0 F 61351707
Ambiguity is an important concept in the MIRO-pipeline, it is therefore crucial that this concept is properly understood. In a nutshell, ambigutiy is the number of equal good mapping positions for a single Solexa-read. Equal good in this context refers to the number of mismatches. In the MIRO-pipeline all unambiguously mapped reads have a ambiguity of "1" and they are provided in a separate output-file. All ambiguously mapped reads, on the other hand, have a ambiguity of ">=2"
Examples:
A read which could be mapped to the H. sapiens genome only once having two mismatches, will have a ambiguity of "1".
A read which could be mapped to the H. sapiens genome three times, always having only one mismatch, will have a ambiguity of "3".
A read which could be mapped to the H. sapiens genome three times having one mismatch and one time having zero mismatches, will have a ambiguity of "1".
A read which could be mapped to the H. sapiens genome three times having one mismatch and two times having zero mismatches, will have a ambiguity of "2".
A wiggle formated file which is accepted by most genome browsers. The track informations may easily edited manually directly in the output file.
For example:
track type=wiggle_0 name="unknown" description="variableStep format" visibility=full variableStep chrom=chr7 span=1000 156001 30 763001 5 897001 5 1029001 154 1085001 10 1537001 5 1850001 10 1879001 7 2069001 15 2116001 5 2361001 13 2384001 5 4817001 11 variableStep chrom=chr20 span=1000 255001 13 336001 7 762001 6 930001 11 1113001 7 1321001 5 1810001 9 2391001 12 2581001 96 2582001 6 variableStep chrom=chr14 span=1000 18413001 9 18755001 10 19854001 5 19861001 5 19881001 274 19895001 6 19952001 8 20147001 5 20151001 186 20163001 74
Perl 5.8 or higher
Robert Kofler
Heinz Himmelbauer
robert.kofler at crg.es