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汕头大学海洋科学接受调剂
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sherry_zhang

新虫 (初入文坛)

[求助] Small RNA-seq原始数据怎么处理?

我现在有small RNA-Sequencing 的原始数据,fastq的数据格式的,我想得到miRNA 的ID名和表达信息,该怎么做啊!急求!
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sherry_zhang

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我用tophat进行比对,为什么都没有比对上,用的是ensemble上的人类参考序列

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4楼2015-11-04 16:59:51
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yingyangyang

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基于小RNA-Seq数据的植物miRNA预测工具
miR-PREFeR: an accurate, fast, and easy-to-use plant miRNA prediction tool using small RNA-Seq data.

Abstract

Summary: Plant microRNA prediction tools that utilize small RNA sequencing data are emerging quickly. These existing tools have at least one of the following problems: 1. high false positive rate; 2. long running time; 3. work only for genomes in their databases; 4. hard to install or use. We develop miR-PREFeR (miRNA PREdiction From small RNA-Seq data), which utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species. We tested miR-PREFeR on several plant species. The results show that miR-PREFeR is sensitive, accurate, fast, and has low memory footprint.
Availability: https://github.com/hangelwen/miR-PREFeR

http://bioinformatics.oxfordjour ... ics.btu380.abstract
2楼2015-08-18 15:15:24
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sherry_zhang

新虫 (初入文坛)

引用回帖:
2楼: Originally posted by yingyangyang at 2015-08-18 15:15:24
基于小RNA-Seq数据的植物miRNA预测工具
miR-PREFeR: an accurate, fast, and easy-to-use plant miRNA prediction tool using small RNA-Seq data.

Abstract

Summary: Plant microRNA prediction tools that ...

我做的是人类的,我想问一下可以用tophat和cufflinks做吗
3楼2015-08-21 09:13:58
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陈爱中

新虫 (小有名气)

【答案】应助回帖

我怎么是公司整理好各个小rna相对积累量的excel表格…

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5楼2015-11-05 07:43:56
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