Alignment script missing. Bowtie2_pipeline.sh doesn't do any alignment.

[markphillippebworth]

The script for bowtie2 within the github doesn't include any documentation of alignment, or the usage of bowtie2. Instead, it just processes a .bam file.

The download and processign the fastq's are well documented, and the processing from .bam files onwards seems clear.
However, there's a gap between fastq's and bam files. Would it be possible to upload your alignment scripts?

I can always turn fastq's to bam files via the methods section, but the actually script is always appreciated.

https://github.com/MiraldiLab/maxATAC_data/blob/main/scripts/ATAC/ATAC_bowtie2_pipeline.sh

[tacazares]

Hey @markphillippebworth,
Here is a snakemake pipeline used to generate the ATAC-seq data.
https://github.com/MiraldiLab/snakeATAC/tree/main

The rule for alignment is here: https://github.com/MiraldiLab/snakeATAC/blob/2c7301e5e75b207bc7cf0ba5dcb673ccde7b6e5b/snakefiles/maxatac.sf#L5