RNA_seq raw-data from open source processing

Question

[Rimma]

Hello, can you please explain to me why when I download SRA file with RNA-seq raw data (SRR8437305) from open source there is no separation for Read1 and Read2, even though it says that it's paired-end sequencing. Moreover, when I process it in FastQC it shows me the following pic, which looks like there is 200 bases and adapter contamination at first 10 bases.

My question is why there is no adapter contamination on the other end and it looks like bias in the middle, so should I trim it from the middle as well? If yes, how can I do it? Also, for further steps of the analysis should I define it as paired-end or single-end since I have only one file.

Thanks a lot!

[GenoMax]

Those first 10 bases are not adapter contamination. This is a very well known bias seen with RNAseq datasets. See this blog entry for more information.

You don't need to do anything with data in first 10 bases. Data should align without any issues.

Answer 1

[ATpoint]

See Fast download of FASTQ files from the European Nucleotide Archive (ENA) for downloading files. If you are going to use fastq-dump use the split-3option. Also please google adapter trimming and search for tutorials towards RNA-seq preprocessing, there are plenty out there, e.g. https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

[Rimma]

Yes, I used just fastq-dump... I will add split-3 option Thanks a lot!

[ATpoint]

It is always recommended to read the documentation first. This can save you quite some time ;-)