1 Data

1.1 Introduction of the common data

1.1.1 Wide Matrix

Each column in Wide format is a variable, which is more like common gene expression data. For example, each row is a gene, and each column is a sample. It is suitable for a regular matrix and has good readability.

1.1.2 Long Matrix

The simplest format of Long format is two columns, one column contains all variable types, as in the sample mentioned earlier, one column contains all values. The common gene expression matrix is converted from Wide format to Long format and has three columns, one column is GeneID, one column is sample name, and the other column (usually column name is value) is the gene expression value, which represents the expression level of the corresponding gene in the corresponding sample. This format is convenient for program processing and is also suitable for irregular data.

1.1.3 FASTA

1.1.4 FASTQ

1.2 Long To Wide Matrix

Long To Wide Matrix can transform a long matrix to a wide matrix.

In the demo1, paste three-column matrix including the expression of genes in different samples with long matrix format.

In the transforming parameters:

  • Transform the column containing genes in long matrix to the row of wide matrix by selecting the option of Gene in the Column used as rownames in wide format matrix parameter;

  • Transform the column containing the value of samples in long matrix to the column of wide matrix by selecting the option of Sample in the Column used as headers in wide format matrix parameter;

  • Transform the column containing the expression of genes in long matrix to the value of wide matrix by selecting the option of Expr in the Column used as numeric values parameter;

  • Specify “0” to replace the missing value by inputting 0 in the textarea of Specify to replace missing values parameter;

  • Do not transfer all numbers to integer values by selecting No in the Transfer all numbers to integer values parameter;

  • Do not remove rows containing only zeros by selecting No in the Remove rows containing only zeros parameter.

1.3 Merge matrixes

Merge matrixes can merge two matrixes based on the columns shared by the two matrixes.

In the demo1, paste matrix1 including the expression of genes in different samples and matrix2 including the number of cells in different samples.

In the transforming parameters:

  • Specify one column name in matrix1 as common column for merging by selecting the option of ID in the Column used for merging in left matrix parameter;

  • Specify one column name in matrix1 as common column for merging by selecting the option of ID in the Column used for merging in right matrix parameter;

  • Merge two matrixes common rows based on columns shared by the two matrixes by selecting the option of inner in the Combined type parameter.

1.4 Wide To Long Matrix

Wide To Long Matrix can transform a wide matrix to a long matrix.

In the demo1, paste a matrix including the expression of genes in different samples with wide matrix format.

In the transforming parameters:

  • Specify the names of column which would stay as original after transfer by selecting the option of ID in the ID variable parameter;

  • Specify “Expression” to be the column name in transferred long matrix to save all values by inputting Expression in the textarea of Column name in long matrix to save all values parameter;

  • Specify “Gene” to be the column name of all measured variables in transferred long matrix by inputting Expression in the textarea of Column name in long matrix to save all values parameter.

1.5 Reverse Complement Sequences

Reverse Complement Sequences can output the complementary sequences, the reverse complementary sequences, or the reverse complementary sequences of the input sequences.

In the demo1, paste a sequence with FASTA format.

In the transforming parameters:

  • Specify the sequence is DNA sequence by selecting the option of DNA in the Type of base sequences parameter;

  • Specify output the reverse complementary sequences of the input sequences by selecting the option of Reverse Complementary in the Operation type parameter.

1.6 RNA translation

RNA translation can translate RNA sequence to protein sequence.

In the demo1, paste a sequence with FASTA format.

In the transforming parameters:

  • Specify translate sequences from the first frame by selecting the option of the first frame in the Frames used for translation parameter;

  • Specify translate sequences in positive strand by selecting the option of Forward chain in the Select sequence strand parameter;

  • Specify standard codon table by selecting the option of Standard in the Codon table parameter.

1.7 Reverse File Line

Reverse File Line can reverse the line of file.

In the demo1, paste a matrix including the expression of genes in different sample.

In the transforming parameters: - Do not output the first line of the file in reverse by selecting the option of True in the Header parameter.