Illumina small RNA-Seq
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下载链接：
https://figshare.com/articles/dataset/Illumina_small_RNA-Seq/13852256
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资源简介：
Small RNA sequenced on Illumina platform were annotated.Illumina raw reads were quality-checked with FastQC, adapters and contamination removed with Cutadapt, quality-checked again, reads mapped to the tufted duck reference genome with STAR, transcripts assembled with Cufflinks, nucleotide sequences extracted with bedtools, small RNA predicted in the reference genome and annotated with assembled small RNA using the Infernal tool cmscan, output converted to gff3 with tblout3gff3.pl.cutadapt options: ${-m 9 -q 20 -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC}STAR options: ${--outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --outSAMheaderHD @HD VN:1.4 SO:coordinate --quantMode GeneCounts --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1}cmscan options (brain*): ${-Z 2.420214 --cut_ga --rfam --nohmmonly --tblout ncRNA_cmscan_brain.tblout --fmt 2 --clanin Rfam.clanin Rfam.cm}*Z-value depends on input data
创建时间：
2021-10-21
