Hi all,
I have received some RNA-seq data and after looking through the data, it seems that the adaptors have not been fully trimmed.
I used grep with a portion of the adaptor sequence one my fastq files and the TruSeq Illumina universal adaptor seems to be present in my reads as well as the TruSeq adaptor Index sequences.
After trimming with cutadapt, I ran the trimmed file through fastqc again and it seems the sequence length distribution is no longer the same for all the reads.
Prior to trimming, all the reads were 101bp, and now there are reads that are shorter and I have attached the graph I get for the trimmed reads.
Previous RNA-seq data I have received have been trimmed already, so I am new to trimming adaptor sequences. Below is the code I used for trimming the adaptors.
cutadapt -a GATCGGAAGAGCA -g GCTCTTCCGATCT -o "PATH to trimmed file" "PATH to file"
Is it normal to have non-uniform reads after trimming or do they need to all be uniform length for downstream alignment and analysis?
Thanks
I have received some RNA-seq data and after looking through the data, it seems that the adaptors have not been fully trimmed.
I used grep with a portion of the adaptor sequence one my fastq files and the TruSeq Illumina universal adaptor seems to be present in my reads as well as the TruSeq adaptor Index sequences.
After trimming with cutadapt, I ran the trimmed file through fastqc again and it seems the sequence length distribution is no longer the same for all the reads.
Prior to trimming, all the reads were 101bp, and now there are reads that are shorter and I have attached the graph I get for the trimmed reads.
Previous RNA-seq data I have received have been trimmed already, so I am new to trimming adaptor sequences. Below is the code I used for trimming the adaptors.
cutadapt -a GATCGGAAGAGCA -g GCTCTTCCGATCT -o "PATH to trimmed file" "PATH to file"
Is it normal to have non-uniform reads after trimming or do they need to all be uniform length for downstream alignment and analysis?
Thanks
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