Questions tagged [trinity]

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Trinity de novo transcriptome assembly: samtools view failed to add PG line to the header

I have assembled the transcriptome a plant species using Trinity. Here is the command: ...
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Assembling all transcripts for an individual gene? (using single sequence to seed the assembly)

Let's say I have a candidate gene and I believe that in an individual sample, the genome sequence differs from the reference which then interferes with alignment. Is there a way for me to do a "...
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