The verbose option crashes terminal every time I use it (after a few hours, but before the mapping is done), so I don't know about that.
The fastqc plots of kmer and overrepresented sequences are rather odd looking, but as this is a transcriptome it is unclear to me what the expectation should be, although from what I can tell by googling around what I have is not unusual for a transcriptome. I did not use barcodes for this dataset.
I have tried doing some additional quality filtering to see if that makes a difference. I will report back on that.
Just mapping the reads that do map and completing the pipeline does produce contigs that blast appropriately.
The fastqc plots of kmer and overrepresented sequences are rather odd looking, but as this is a transcriptome it is unclear to me what the expectation should be, although from what I can tell by googling around what I have is not unusual for a transcriptome. I did not use barcodes for this dataset.
I have tried doing some additional quality filtering to see if that makes a difference. I will report back on that.
Just mapping the reads that do map and completing the pipeline does produce contigs that blast appropriately.
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