...--------------------------------------------[2019-04-28 05:49:42] Checking for Bowtie Bowtie version: 2.2.7.0[2019-04-28 05:49:44] Checking for Bowtie index files (genome).. Found both Bowtie1 and Bowtie2 indexes.[2019-04-28 05:49:44] Checking for refe...
...3900000 SAM alignment record pairs processed.Warning: Mate records missing for 270457 records; first such record: <SAM_Alignment object: Paired-end read 'A00224:87:H5WHYDSXX:1:2474:9118:3098' aligned to utg9_pilon_pilon_pilon:[3553256,3553424)/+>.24000000 SAM alignment record pairs processed.2...
...Each undeclared identifier is reported only oncecram/cram_io.c:684: error: for each function it appears in.)cram/cram_io.c:684: warning: implicit declaration of function ‘lzma_easy_buffer_encode’cram/cram_io.c:684: error: ‘LZMA_CHECK_CRC32’ undeclared (first use in this function)cram/cram_io...
** inst
** byte-compile and prepare package for lazy loading
Error in get(x, envir = ns, inherits = FALSE) :
object 'message_wrap' not found
Error: unable to load R code in package ‘ggtern’
Execution halted
ERROR: lazy loading failed for package ‘ggtern’
* removing ‘/share/bios...
...r of PEER factors was selected as function of sample size (N):
15 factors for N < 15030 factors for 150 ≤ N < 25045 factors for 250 ≤ N < 35060 factors for N ≥ 350
根据文章的提示，使用的是peer这个工具：
peer有两个版本，python和R，我们这里使用R包封...
...d not found: default_channels:
manager@bl8vbox[manager] - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zsh: no such file or directory: https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
manager@bl8vbox[manager] - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
zsh...
...the TCGA Data Portal hosted by the TCGA Data Coordinating Center (DCC), in which uses as references GRCh37 (hg19) and GRCh36 (hg18).
GDC harmonized database: data available was harmonized against GRCh38 (hg38) using GDC Bioinformatics Pipelines which provides methods to the standardization of biosp...
... set event column name must 0 or 1 code format [required] -v variate [variate ...], --variate variate [variate ...] variate for cox analysis [required] -P predict.time [predict.time ...], --p...
... GO enrichment analysis data,the data with
columns for 'category','ID','term',adjusted
p-value('adj_pval') and 'genes'[required]
-d DEG_DATA, --deg_data DEG_DATA
input the result of differential expression analysis
...
... by qRT-PCR.
There were three biological and three technicalreplicates performed for each sample. The relative expression levelswere evaluated by 2-ΔΔCT. GraphPad software was used for the statistical analyses.
作者是用的2-ΔΔCT的方法做的数据分析，可是结果怎么会是负数...