Today I read more about using Trinity and functional genomics as well as got some information back from Nick from Skyline in regards to my high error rate in peak-picking.

Trinity

Steven sent me this code last night (added my notes for what each line does)(GitHub issue #304):
–seqType fq \
the sequence reads are of fastq type (there is a quality value given to each read)
–max_memory 100G
the amount of memory (temporary data storage space) to be allocated to running Trinity
–left /gscratch/srlab/sr320/data/geoduck-RNA-seq/NR012_S1_L001_R1_001.fastq, /gscratch/srlab/sr320/data/geoduck-RNA-seq/NR012_S1_L002_R1_001.fastq
look at the left reads of the paired data
–right /gscratch/srlab/sr320/data/geoduck-RNA-seq/NR012_S1_L001_R2_001.fastq, /gscratch/srlab/sr320/data/geoduck-RNA-seq/NR012_S1_L002_R2_001.fastq
look at the right reads of the paired data
–trimmomatic
trim the reads for quality
–CPU 28
number of computer processing units to allocate to running Trinity`

I have been looking at this page: Running Trinity

And Steven also sent me this paper: OPPORTUNITIES IN FUNCTIONAL GENOMICS: A PRIMER ON LAB AND COMPUTATIONAL ASPECTS
And a link to praciticing navigating Command Line: Navigating Command Line

Skyline error update

Nick from Skyline responded to my request for information on my high error rates. I’m not 100% sure I understand what is going on, but I forwarded the response to Emma and am looking into what this means right now.

Link to my post and Skyline Support Team’s responses: here

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