bowtie2_alignment

Arguments

Mapping reads to a reference genome with Bowtie2 alignment of FASTQ sequencing reads files from high-thoughput sequecing, and visulizing results.

Required arguments:

  • -f, --fastq: Path to directory containing FASTQ files.

either

  • -i, --bowtie2_index_pathway: Input file folder of Bowtie2 reference genome indexing files.

or

  • -r, --reference: Input reference genome FASTA file for the creation of Bowtie2 reference genome.

Optional arguments:

  • -o, out_dir: Output directory, default = current working directory.

  • -s , --spike_in: If the alignment is spike-in, default = False.

  • -m , --merge: Merges technical replicates, default = False.

Example Usage:

Example with existing bowtie2 indexing files:

$ epimapper bowtie2_alignment -f /Users/me/my_fastq_files -i /Users/me/in_folder/bowtie2_index_hg38 -o /Users/me/results

Example with reference genome FASTA file:

$ epimapper bowtie2_alignment -f /Users/me/my_fastq_files -r /Users/me/in_folder/hg38.fna -o /Users/me/results

Example of spike-in alignment:

$ epimapper bowtie2_alignment -f /Users/me/my_fastq_files -s True -i /Users/me/in_folder/bowtie2_index_ecoli -o /Users/me/results

Example usage with technical replicates:

$ epimapper bowtie2_alignment -f /Users/me/my_fastq_files -m True -i /Users/me/in_folder/bowtie2_index_hg38 -o /Users/me/results

Output

Like all the other functions in EpiMapper Python package, the function will create a main Epimapper output directiry, if it is not already present in the chosen output directory. Further, this function will create directories based on if the alignment is considered a “spike-in” alignment (if the -s parameter is set to True) or not. If not the output directroy structure will as shown below. Here, the “sam” directory will contain the aligned sam files, and the “bowtie2_summary” folder will contian text files for each sample with alignment statistics. These text files are used to create the “bowtie2_alignment_rep.csv” located in the “summary_tables” folder. Lastly, a PNG image file containing boxplots of sequencing depths, mapped fragments and alignment rate is created and also stored in the “summary_tabels” folder.

Epimapper
|- alignment/
|   |- sam
|   |-  bowtie2_summary
|- summary_tables
|   |- Sequencing_depth_ref.png
|   | - bowtie2_alignment_rep.csv

However if the the -s parameter is set to True, the output folders will have differnt name, but contian the same types of files.

Epimapper
|- alignment
|   |- sam_spike_in
|   |-  bowtie2_summary_spike_in
|- summary_tables
|   |- Sequencing_depth_spike_in.png
|   | - bowtie2_alignment_spike_in.csv

If spike-in alignment is performed after alignment to reference genome the summary table and figure will contain both results.