PANDA姐的转录组入门(2):读文章拿到测序数据
文章
AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors1
数据下载
# https://www.ncbi.nlm.nih.gov/gquery/?term=GSE81916
# esearch -db sra -query PRJNA299273 | efetch -format runinfo > runinfo.txt # 这个命令是把所有的结果放到一个文件里,也可以通过 https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA323422下载SRR的编号
# cat runinfo.txt | cut -f 1 -d ',' | grep SRR > sra.ids
# ~/biosoft/sratoolkit.2.8.2-1-centos_linux64/bin/prefetch --option-file sra.ids # 数据存在/home/shenmy/ncbi/public/sra这个文件下面,找了半天
mkdir /mnt/d/rna_seq/data && cd /mnt/d/rna_seq/data
perl -lne '$id=substr($_,0,6);print "axel ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/$id/$_/$_.sra"' SRR_Acc_List.txt >sra_down.sh
bash sra_down.sh
# 改成用axel下是因为prefetch下载总是不成功
ls *.sra|while read id;do(/mnt/d/Software/Biosoft/sratoolkit/sratoolkit.2.8.2-1-ubuntu64/bin/fastq-dump --split-3 $id);done
rm *.sra
chmod u-w *
https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA323422
这是一个随意的视频~
https://v.qq.com/txp/iframe/player.html?vid=l0524xeztfw&width=500&height=375&auto=0
重点注意
一个RNA-seq的反思:老司机翻车2 http://www.bio-info-trainee.com/2275.html
其他学习笔记
生信菜鸟团:https://mp.weixin.qq.com/s/LN_rQNSHdcdKb25s4mFeqw
hoptop:http://www.biotrainee.com/thread-1829-1-1.html
青山屋主:http://fbb84b26.wiz03.com/share/s/3XK4IC0cm4CL22pU-r1HPcQQ2FSGeS3LE4tM2rg0A-1qRcP-
Hu J, Khodadadijamayran A, Mao M, et al. AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors[J]. Nature Communications, 2016. ↩
一个RNA-seq的反思:老司机翻车http://www.bio-info-trainee.com/2275.html ↩
~ 好好学习,天天向上 ~
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