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trimming a paired end sra

Hi all, For the paired end sequences I took from GEO dataset, I run FastQC and For the forward read the fastqc results is like below: Forward read

Forward read

For the reverse read the fastqc results is like below: Reverse read

enter image description here

As you can see from the screenshots, the reverse read length is 8. And I should run trimmomatic before STAR aligner. So my questions are; 1) How should I run trimmomatic for reverse read (It looks like only the adapter sequence present in the fastq file) 2) In the forward read fastqc results there is no overrepresented sequences shown, the default adapters in trimmomatic will work on them

adapter fastqc rna-seq
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updated by GenoMax GenoMax • written by biology_inform • biology_inform

1 answer

And I should run trimmomatic before STAR aligner.

Not strictly. STAR will handle any adapter sequence present and remove it during alignments.

the reverse read length is 8

This does not sound right. This file may simply be illumina indexes.

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written by GenoMax GenoMax

Not strictly. STAR will handle any adapter sequence present and remove it during alignments.

I didnt know that, so I am just running STAR thanks

For the second thing, I thought so too.

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written by biology_inform • biology_inform

I have one more question, when I open the file none of sequences are identical. I couldnt understand what does it mean enter image description here

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written by biology_inform • biology_inform

I don't know the meaning of the R2 files with 8 bp sequences either. Perhaps this is related to the type of data you are working with. If there is an associated publication, take a look at that.

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written by GenoMax GenoMax

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