Question: Information on "sample_name.cnt" obtained by an RSEM analysis
0
gravatar for umekage
21 days ago by
umekage0
Japan
umekage0 wrote:

Hello, I obtained a "sample_name.cnt" in a newly created "sample_name.stat" directory after an RSEM-1.3.3 analysis. Shown below is the content of the "sample_name.cnt". What do these numbers mean? Thank you in advance for your kindness.

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
.
.
.
rsem rna-seq count • 505 views
ADD COMMENTlink modified 19 days ago • written 21 days ago by umekage0
1
gravatar for umekage
19 days ago by
umekage0
Japan
umekage0 wrote:

The format and meanings of each field are described in "cnt_file_description.txt" under RSEM directory.

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

https://github.com/bli25broad/RSEM_tutorial

Here is the transcript.

  # '#' 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
ADD COMMENTlink modified 15 days ago • written 19 days ago by umekage0
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