PHP Code:
bismark_v0.12.5/bismark_genome_preparation --path_to_bowtie ~/scripts/bowtie-1.1.0/ --verbose .
bismark_v0.12.5/bismark -n 1 -l 50 --path_to_bowtie ~/scripts/bowtie-1.1.0/ ~/ngs/bismark-hsa/ test_data.fastq
The genome sequence are in a fasta file hg19.fa, if anything, the working directory when I prepare the genome don't have this file, but have a link to hg19.fasta in other folder.
This is a part of the report:
Final Alignment report
======================
Sequences analysed in total: 10000
Number of alignments with a unique best hit from the different alignments: 0
Mapping efficiency: 0.0%
Sequences with no alignments under any condition: 10000
Sequences did not map uniquely: 0
Sequences which were discarded because genomic sequence could not be extracted: 0
Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT: 0 ((converted) top strand)
CT/GA: 0 ((converted) bottom strand)
GA/CT: 0 (complementary to (converted) top strand)
GA/GA: 0 (complementary to (converted) bottom strand)
Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
======================
Sequences analysed in total: 10000
Number of alignments with a unique best hit from the different alignments: 0
Mapping efficiency: 0.0%
Sequences with no alignments under any condition: 10000
Sequences did not map uniquely: 0
Sequences which were discarded because genomic sequence could not be extracted: 0
Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT: 0 ((converted) top strand)
CT/GA: 0 ((converted) bottom strand)
GA/CT: 0 (complementary to (converted) top strand)
GA/GA: 0 (complementary to (converted) bottom strand)
Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
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