User: E

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E0
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Posts by E

<prev • 5 results • page 1 of 1 • next >
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Read counts from bam file without available annotation file
... Hi, I have small RNA data from gonadal tissue. A high amount of these sRNAs should therefore be piRNAs mapping to tranposable elements. I would like to quantify how many piRNAs correspond to a specific TE. I already mapped my library to TE consensus sequences I got from RepBase. Now I would like ...
pirna rna-seq written 8 months ago by E0
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RepeatMasker database differences between versions.
... Hi, I have a very general questions about repeat masker v4.0.7 and 4.0.8. After running both versions I got very different results. So I looked up the databases they use. Did I understand it correctly that repmasker v4.0.7 uses the dfam-consensus AND the repbase databases but v4.0.8 uses only t ...
opensource libraries repeatmasker repbase written 10 months ago by E0 • updated 10 months ago by WouterDeCoster43k
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miRDeep2: creating Rfam index not possible therefore no Rfam analysis
... Hi, I am trying to run miRDeep2. the subscript make_html.pl uses Rfam to find out more about the sRNAs in question. For this it must creates an bowtie index of the Rfam.fa to map the reads to it. My miRDeep2 however is located in a directory on a server where it does not have the permissions to ...
mirna annotation rfam mirdeep2 written 2.1 years ago by E0
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Comment: C: snRNA annotation in genome
... Hi Puli, thank you for the answer but I am not sure if I can use these tools. As far as I understand it, snoscans looks for 2'-O methylation sno guide RNAs and miR-PREFeR predicts miRNAs in plants. I am looking for a tool that allows me to annotate small RNAs (siRNAs, piRNAs, miRNAs) in a genome ...
written 2.2 years ago by E0
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snRNA annotation in genome
... Hi, I would like to annotate all small RNAs in a genome based on different databases (e.g. miRBase) with the purpose of generating a gff file I can use for further analysis (and to practice). I searched for tools to achieve this and my ideal tool has the following qualities: 1. I can provide var ...
annotation small rna rna-seq written 2.2 years ago by E0 • updated 2.1 years ago by Biostar ♦♦ 20

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