Hi everyone,
I am new to the NGS data analysis. I want to trim my raw ngs data to remove junk adapters using Cutadapt package. Now I have two questions.
1.How can I obtain the sequences of the adapters used in my raw reads? I have downloaded the ngs data from SRA database (NCBI))
2. Which sequence of the adapters should be detected and removed (Normal sequence, complement sequence, revers sequence, reverse-complement sequence, or all of them)
Many thanks in advance.
I think Sebastian answers has all you need. I would also recommend using Trimmomatic. It is pretty straight forward with the provided adapter files (https://github.com/timflutre/trimmomatic/tree/master/adapters). Concerning, question 2., it depends a bit on your reads. For example, if you would have paired-end reads with small transcripts and therefore a lot of adapter read-through. But Trimmomatic accounts for all of them with the Palindrome mode (if you have paired-end reads).
I agree with the previous answers; run fastqc on the raw data to get an idea about their quality, what they might contain and what parameters you could use for the trimming, and then Trimmomatic to trim adapters and other low-quality bases. After trimming you can run fastqc again to check if you trimmed what you wanted.
I am in agreement with the above mentioned answers. I also recommend FastX, CutAdapt and Prinseq as alternatives to Trimmomatic. Additionally, if you do not have experience using command line in Linux, you can implements some of the previously mentioned software (FastX, FastQC, Trimmomatic, CutAdapt) on the Galaxy platform.
Hi Mohamad, For your first question, I suggest to use Fastqc but first you should convert your SRA data to fastq format by SRAtoolkit software. For your second question, I suggest to use Trimmomatic.
The Best,
Siavash
Dear all, Many thanks for all your valuable comments. But I think there is a slight misunderstanding about my second question. Indeed, I dont intend to find suitable tools/softwares to remove adapters (such as cutadapt, Trimmomatic or etc). I mean that adapters will demonstrate in which mode (normal, reverse, complementary or reverse complementary) in raw ngs data.
In Trimmomatic software in order to detect adapters, already there are sequences of adapters in couple of files. here I attached these files but actually I do not know their modes.
Mohamad Zamani-Ahmadmahmudi
1. Run the sequences through fastQC It will also detect loads of other weirdness as well including both adaptor and primer contamination, quality problems etc. All sequences for the contaminants are present in the config file called "contaminant_list.txt"
2. This link might be helpful
http://seqanswers.com/forums/showthread.php?t=198
- Badges
- Science method