User: matthew.johnson

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Posts by matthew.johnson

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salmon gene quant to DESeq2
... Hi again - I successfully ran salmon on my fastq files, including gene-level summary via a simple two-column map file of transcript-to-gene-ID. This gives me an output like this for each fastq: Name Length EffectiveLength TPM NumReads ENSMUSG00000114165 2016 1815.57 0.0732938 3.29409 I tr ...
galaxy rna-seq written 8 days ago by matthew.johnson10
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Comment: C: Salmon: no built-in index reference transcriptome available
... Thanks Jen. For others: I downloaded the mouse cDNA fasta file here: ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz I uploaded to Galaxy, ran it through the NormalizeFasta tool, and used it as the reference transcriptome for Salmon. Running now.. ...
written 9 days ago by matthew.johnson10
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Salmon: no built-in index reference transcriptome available
... I'm trying Salmon for the first time and when I select "Use a built-in index" for the reference transcriptome it says "No options available." Perhaps these haven't been loaded/indexed for salmon yet? Alternatively, what's the easiest way to import the right fasta format to my history, e.g., from UC ...
galaxy rna-seq written 9 days ago by matthew.johnson10 • updated 9 days ago by Jennifer Hillman Jackson22k

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