User: diego.carvalhoalvarez

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Posts by diego.carvalhoalvarez

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Comment: C: Rsubread inbuilt annotation
... So far I could not find an ncbi annotation file as desired so I decided to stick with Gencode, Ensembl assemblies and the inbuilt annotation. I tried both out of curiosity and they work as expected except for a detail...the percentage of successfully assigned alignments using Gencode primary assembl ...
written 6 months ago by diego.carvalhoalvarez0
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Comment: C: Rsubread inbuilt annotation
... I think it should be what you stated, a mismatch between ncbi genome and the inbuilt annotation. According to the documentation: "The in-built annotations are a modified version of NCBI RefSeq gene annotations. We downloaded the RefSeq gene annotations from NCBI ftp server (eg. RefSeq annotation for ...
written 6 months ago by diego.carvalhoalvarez0
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Comment: C: Rsubread inbuilt annotation
... Thank you very much for your response. I used NCBI genome to build the index so they should match... (I only copied part of the output as the result is the same for all the files)... ...
written 6 months ago by diego.carvalhoalvarez0
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Rsubread inbuilt annotation
... Hi. I have been working with mouse RNA-Seq data and I aimed to use Rsubread package to align, annotate and quantify the reads. My issue is that whenever I use the inbuilt annotation for the mouse genome practically none of the reads are mappped: ``` align (index = "GRCm38.p4", readfile1 = all.fastq1 ...
rsubread featurecounts written 6 months ago by diego.carvalhoalvarez0 • updated 6 months ago by Gordon Smyth39k

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