Hello,
This is my first time posting, but I have had a lot of help from the SEQanswers forums while browsing anonymously in the past, so thanks to everyone who has asked and answered questions on here.
We recently got some RNA-seq done by a commercial company, and I ran FastQC to check the quality before adapter removal and trimming. We submitted 36 samples for paired-end sequencing, 150bp, on an Illumina NextSeq 500. About 11 of our 36 samples had per-tile sequence qualities like the attached, with smears of poor quality in four places. All of them have the poor quality line around tile 21409. This is only the second time I have handled RNA-seq data, and the first batch was from a different centre and was much better quality (at least with respect to the per-tile sequence quality). My question is, is this something I should raise with the company who did the sequencing, or is it typical variation that won't cause any trouble further down the line? I am planning to tidy the data with Trimmomatic before aligning.
Many thanks in advance.
This is my first time posting, but I have had a lot of help from the SEQanswers forums while browsing anonymously in the past, so thanks to everyone who has asked and answered questions on here.
We recently got some RNA-seq done by a commercial company, and I ran FastQC to check the quality before adapter removal and trimming. We submitted 36 samples for paired-end sequencing, 150bp, on an Illumina NextSeq 500. About 11 of our 36 samples had per-tile sequence qualities like the attached, with smears of poor quality in four places. All of them have the poor quality line around tile 21409. This is only the second time I have handled RNA-seq data, and the first batch was from a different centre and was much better quality (at least with respect to the per-tile sequence quality). My question is, is this something I should raise with the company who did the sequencing, or is it typical variation that won't cause any trouble further down the line? I am planning to tidy the data with Trimmomatic before aligning.
Many thanks in advance.
Comment