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经过 RSEM-1.3.3 分析后，我在新创建的“XXX.stat”目录中获得了一个“XXX.cnt”。

下图是 XXX.cnt 的内容。

0 2726098 0 2726098
1534055 1192043 1993977
9793897 1
0       0
1       732121
2       410181
3       513309
4       610475
5       90206
6       81551
7       63620
8       44947
9       33029
10      21745
11      22282
12      21545
13      13324
14      17247
.
.
.

这些数字是什么意思？

预先感谢您的好意。

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1 回答 1

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每个字段的格式和含义在 RSEM 目录下的“cnt_file_description.txt”中有说明。

http://deweylab.github.io/RSEM/rsem-calculate-expression.html#OUTPUT

https://github.com/bli25broad/RSEM_tutorial

这是成绩单。

# '#' marks the start of comments (till the end of the line) 
# *.cnt file contains alignment statistics based purely on the alignment results obtained from aligners

N0 N1 N2 N_tot   
#  N0, number of unalignable reads; N1, number of alignable reads; N2, number of filtered reads due to too many alignments; N_tot = N0 + N1 + N2     
    
nUnique nMulti nUncertain   
# nUnique, number of reads aligned uniquely to a gene; nMulti, number of reads aligned to multiple genes; nUnique + nMulti = N1;                             
# nUncertain, number of reads aligned to multiple locations in the given reference sequences, which include isoform-level multi-mapping reads

nHits read_type             
# nHits, number of total alignments.                         
# read_type: 0, single-end read, no quality score; 1, single-end read, with quality score; 2, paired-end read, no quality score; 3, paired-end read, with quality score
        
# The next section counts reads by the number of alignments they have. Each line contains two values separated by a TAB character. The first value is number of alignments. 'Inf' refers to reads filtered due to too many alignments. The second value is the number of reads that contain such many alignments
    
0                          N0
...
number_of_alignments       number_of_reads_with_that_many_alignments
...                           
Inf                        N2
于 2020-09-04T06:53:33.833 回答