Name | Modified | Size | Downloads / Week |
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README.txt | 2014-05-15 | 1.7 kB | |
MR_TEST.sh | 2014-05-15 | 44.4 kB | |
Totals: 2 Items | 46.0 kB | 0 |
MR_test: Performs a series of Metarmorphic Relations to FastQ files and runs a short-read alignment software (choices of BWA, Bowtie or Bowtie2) It requires installation of samtools, bwa, bowtie and bowtie2. Usage: ./MR_TEST -program -MR[0-9] [-S or -I] (ref or ref.fa) read1.fastq.gz read2.fastq.gz outputName Options: -program -bwaS BWA with single read -bwaP BWA with paired-end reads -btS Bowtie with single-end reads -btP Bowtie with paired-end reads -bt2S Bowtie2 with single-end reads -bt2P Bowtie2 -MR[0-9] -MR0 Test All MR properties -MR1 Randomly shuffle the reads in the fastq file -MR2 Permute the sequence in the fastq file (A->T,T->A,G->C,C->G) -MR3 Duplicate input sequence and added back to the input file -MR4 Halves the input sequence -MR5 Extend each read by a certain number of nucleotide to the 3' or 5' end of the read with high quality, based on the reference genome -MR6 Remap all unmappable reads against the genome again -MR7 Remap all mappable reads against the genome again (properly paired - only for paired end) -MR8 Increase the quality score for all mapped sequences -MR9 Correct the error in the reads -S Sanger fastq Format -I Illumina fastq Format