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 12 weeks 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 12 weeks 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 12 weeks 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 12 weeks ago by diego.carvalhoalvarez0 • updated 12 weeks ago by Gordon Smyth37k

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