Trimming adapters required for local alignment?

Question

[srhic]

Hello,

I am analyzing some Hi-C data and have a question about quality trimming. When I got the data I was told that the initial QC had already been done so I started analyzing the data without doing any preprocessing. I have already done quite a lot of analysis but recently got to know that the data was checked with fastqc but no trimming was performed. Now I am confused if I should start from scratch with trimmed data and repeat all my analysis or not.

I am using the hicexplorer pipeline for analyzing the data and using bowtie2 to align the data in local alignment mode. Based one some previous posts, it seems that trimming is not necessary when using the local alignment mode but since this is the first time I am working with Hi-C I want to make sure that I follow the correct procedure. I have the option of starting from scratch but as I have already done a lot of analysis it would mean repeating a lot of work. Since my alignment rates were ~96-98% without trimming I am not sure if it is worth doing everything again so I would appreciate any advice.

Thank you

Answer 1

[ATpoint]

Check with fastqc if you even have adapters. If not or only a minor fraction of reads, I guess you'll be fine. fastqc can read BAM files.

[srhic]

Thanks, I didn't know fastqc works on bam files. The adapter content is less than 0.5% so I think I should be fine.

[ATpoint]

Yep, that should be fine I guess.