I am new to Bioinformatics and have been stuck with aligning my data for 3 weeks! I feel like I have tried everything. I would like to align my ATAC-seq data using Bowtie2. Now I have previously done that using the command:
bowtie2 -x "name of index" -1 fast.reads -2 fast.reads -S name.sam
However, now when I run this command it updates/modifies the bowtie2 executable file for some reason!
The full command that I use is exactly as below:
cd bowtie2-2.3.4-mingw-x86_64/example/reference bowtie2-2.3.4-mingw-x86_64bowtie2 -x GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index -1 bowtie2-2.3.4-mingw-x86_64/example/index/out.1.fastq -2 /bowtie2-2.3.4-mingw-x86_64/example/index/out.2.fastq -S 1.sam
Thanks so much for your help!