gravatar for a.hayat20

2 hours ago by

Hi all,

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!

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modified 2 hours ago

by

h.mon32k

written
2 hours ago
by

a.hayat200



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