Question: Calculation of number of raw reads, Q30, GC content for raw data QC
0
gravatar for lidanqing1990
22 months ago by
lidanqing199010 wrote:

Hi, all I am new in bioinformatics and need your help on a simple question. I got two fastq files (forward.fastq and reverse.fastq) of one sample by RNA-seq. Then, I used fastqc to treat with two fastq files, separately and I could calculate number of raw reads, Q30, GC content of each fastq file. So how to calculate number of raw reads, Q30, GC content for this sample? Should I get the sum of raw read number of two fastq files for raw reads number of this sample, the mean value of Q30 or GC content of two fastq files for Q30 or GC content of this sample?

I was so confused about that. Thank you for your help.

rna-seq • 1.1k views
ADD COMMENTlink written 22 months ago by lidanqing199010
0
gravatar for genomax
22 months ago by
genomax65k
United States
genomax65k wrote:

Number of raw reads is in the summary at the top of each FastQC report. Remember that you are sampling the same fragment from two ends (hence the forward and reverse reads). The values you are seeing in the files are for that sample.

ADD COMMENTlink written 22 months ago by genomax65k

yes, I got it. But Q30 or GC content of two fastq files is different, so which one is Q30 or GC content of this sample?

ADD REPLYlink written 22 months ago by lidanqing199010

I'd report both forward and reverse Q30 and GC from FastQC, so four numbers. This is for quality control, so having all values available will avoid "hiding" bad data.

ADD REPLYlink written 22 months ago by Sean Davis25k

But Q30 or GC content of two fastq files is different,

Can you provide the numbers for two files? As suggested by @Sean provide all numbers if you are giving them to someone.

ADD REPLYlink modified 22 months ago • written 22 months ago by genomax65k

Thanks you both. Q30 and GC content in forward fastq file are 50 and 92.54%, respectively and in reverse fastq file are 50 and 90.19%, respectively. Is these information enough? Is there a way to just get these information of the sample? Should I merge these two fastq files and then use fastqc to treat with the merged fastq file?

ADD REPLYlink written 22 months ago by lidanqing199010
1

These numbers are functionally the same. No, I would not merge the fastq files. I would report two Q30 numbers and two GC numbers. In all cases where the experiment "worked" as expected, the numbers for read 1 and read 2 will be quite similar. If they are not, you NEED to know that.

ADD REPLYlink written 22 months ago by Sean Davis25k

Thanks again @Sean, I got it.

ADD REPLYlink written 22 months ago by lidanqing199010
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