Mapping FASTQ files

To map FASTQ files using the API, we will use the module.


First, we need to decide which mapper to use, and under what circumstances an unaligned read should be truncated and re-mapped to the genome. The SimpleBowtie2Mapper, for example, only attempts to align a read once and does no iterative mapping. The Bowtie2Mapper resubmits unaligned reads and reads with a low score, There are equivalent mappers for BWA named SimpleBWAMapper and BWAMapper, but here we choose the Bowtie2Mapper. It requires only the path of the corresponding bowtie2 index:

mapper = map.Bowtie2Mapper('hg19_chr18_19/hg19_chr18_19',
                           threads=4, min_quality=30)

The threads parameter controls how many threads are given to each bowtie2-align process. By using a .bam ending, the output is converted to a BAM file at the end of mapping automatically.

Iterative mapping

Now we can use to start the actual mapping process:

sam_folder = mkdir(os.path.join(output_folder, 'sam'))
sam_1_file = map.iterative_mapping('SRR4271982_chr18_19_1.fastq.gzip',
                                   os.path.join(sam_folder, 'SRR4271982_1.bam'),
                                   threads=1, min_size=15, step_size=10,
sam_2_file = map.iterative_mapping('SRR4271982_chr18_19_2.fastq.gzip',
                                   os.path.join(sam_folder, 'SRR4271982_2.bam'),
                                   threads=1, min_size=15, step_size=10,

Note that we are calling iterative mapping twice, independently for each FASTQ file, as appropriate for a Hi-C experiment. min_size determines the minimum size of a truncated read after which it will be discarded, while step_size determines the truncation amount.


When downloading FASTQ files from SRA using SRAtools, e.g. with fastq-dump, do not use the -I / --readids option, which appends .1 or .2 to the read name. This interferes with the sorting and read pairing step in FAN-C. Read names of the two mates must be identical.

By providing a restriction_enzyme name, we enable ligation junction splitting. Each read will be scanned for a predicted ligation junction of the provided restriction enzyme and if one is encountered, it will be split at the junction before alignment. This can greatly increase alignment rates, especially for longer reads.

SAM/BAM sorting

After the mapping is complete, we can sort the files by read name for further processing.

from import sort_natural_sam
sorted_sam_1_file = sort_natural_sam(sam_1_file)
sorted_sam_2_file = sort_natural_sam(sam_2_file)

The above command replaces the original file with the sorted version. You can use the output_file parameter to output to a different file, if you prefer to keep the unsorted version.