Transcriptomics

Source code for RNA MS analysis.

Files

Program.cs

• Extracts intensities of all fragments present in the raw file
• Note: When running the script for unmodified RNA, comment out the section regarding modifications in Program.cs (line 33-40)

Change these variable values:

• outputPath
• rawfilePath
• oligonucleotide: G, U, A, C sequence without modifications

Program(InternalFragments).cs

• Extracts intensities of all internal fragments (fragments without either terminus) present in the raw file
• Utilizes InternalFragMZ_21nt.txt for m/z values needed to extract the corresponding intensity
• Note: To run Program(InternalFragments).cs, rename Program.cs to Program(fragments).cs and rename Program(InternalFragments).cs to Program.cs

Change these variable values:

• outputPath
• rawfilePath
• SteamReader parameter: for Program(InternalFragments).cs only (line 30), to specify the location of the text file

InternalFragMZ_21nt.txt

• Text file contains calculated m/z of all possible internal fragments of the 21nt RNA.
• First row contains the charge state.
• First column contains the monoisotopic mass of an internal fragment
• Second column contains the position of the internal fragment.