The gto_fastq_variation_map identifies the variation that occours in the sequences relative to the reads or a set of reads.
For help type:
./gto_fastq_variation_map -h
In the following subsections, we explain the input and output paramters.
The gto_fastq_variation_map program needs FASTQ, FASTA or SEQ files to be used as reference and target files.
The attribution is given according to:
Usage: ./gto_fastq_variation_map ... [FILE]:<...> [FILE]:<...>
./gto_fastq_variation_map: a tool to map relative singularity regions
The (probabilistic) Bloom filter is automatically set.
-v verbose mode,
-a about CHESTER,
-s bloom size,
-i use inversions,
-p show positions/words,
-k k-mer size (up to 30),
[rFile1]::<...> reference file(s),
[tFile1]::<...> target file(s).
The reference files may be FASTA, FASTQ or DNA SEQ,
while the target files may be FASTA OR DNA SEQ.
Report bugs to <{pratas,raquelsilva,ap,pjf}@ua.pt>.
An example of a reference file (Multi-FASTA format) is:
>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCC
CGGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGG
AAGTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGT
GCCGCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCC
CAGCTAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA
ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCCCCTGGAGGG
TGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGCCTCCTGACTTTCCTCGCT
TGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGG
AAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTG
CAAATAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA
An example for the target file (FASTQ format) is:
@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=60
GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIII
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I
The output of the gto_fastq_variation_map program is a text file identifying the relative regions.
Using the inputs above, an output example for this is the following:
1111111111111111111111111111100000000000000000000000000000001111111111111111111
11111111110000000000000000000000000000000000000000000