Entering edit mode
2.3 years ago
tea.vuki
▴
10
Hello, it's me again with some question! :( I have started with two BAM files: one RNA-seq, the other one WXS and by following the tutorial I did FastQC analysis on those files. However, for my own curiosity I decided to convert these BAM files to FASTQ files with SBG. After that I run the FastQC on FASTQ files and I got different results. Why did this happen? Everything was done on the same platform.
Since the data files are from two different types of samples they are unlikely to produce identical FastQC results. (I assume WXS = whole exome sequencing?)
Yes, but that's not what I am talking about I had one file WXS.bam and other one WXS.fastq, one file RNAseq.bam and other one RNAseq.fastq. I compared FastQC of WXS.bam and WXS.fastq and they are completely different. And I converted that WXS.bam file to WXS.fastq, so I don't get why they are so different.
This clarification adds important information compared to what you had written in the original post.
When you did the conversions did you make sure that you
a. Name sorted the BAM files
b. Removed secondary/supplementary alignments ensuring that there are no duplicate records?
This comparison seems unnecessary, especially if you had created the BAM files starting with the fastq in first place.
I did both of those while converting. I didn't started with fastq files, all I got on that platform was BAM files and then in order to do a little research and figure out what to do next I explored the platform a little bit. Therefore, I converted BAM to fastq, mainly in order to see how Trim Galore works. Then I figured why not do FastQC on fastq files, out of curiosity. I ended with unexpected results and now I don't even know is it ok to do trimming on those converted fastq files since FastQC report is so different from what I started with. I mean, comparison is unnecessary, I was just curious why bam and fastq files produce different FastQC report and is that generally the case or I did something wrong.