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compile from git clone

First, clone the source code by doing the following (in an empty folder):

git clone [email protected]:Shao-Group/rnaseqtools.git .

Then, compile with the following commands

aclocal
autoconf
autoheader
automake -a
./configure
make

compile from releases

This repo rnaseqtools provides a set of tools to process transcripts (mainly in gtf format). To compile these tools, you first need to download the source code of the latest release from here, then use the following commands to compile:

./configure --prefix=/path/to/your/install/folder
make
make install

gtfmerge

This tool is to compute the union of a collection of sets of transcripts. Two transcripts are defined as identical if they are from the same chromosme, on the same strand, and having the same intron chain coordinates. The usage of gtfmerge is as follows:

gtfmerge union <input-gtf-list> <output-gtf-file> [-t <integer>] [-n]
  1. The parameter input-gtf-list is mandatory, which provides a list of gtf files (each line specifies a file name). Each gtf file gives a set of transcripts.
  2. The parameter output-gtf-file is mandatory, which contain the merged transcripts, also in gtf file format.
  3. -t <integer> is optional. If it is provided, then the multiple-threading mode will be open, and the specified number of threads will be used.
  4. -n is optional. If it is used, then the number of appearance of each unioned transcript (i.e., how many input gtf files contain this transcript) will be recorded and reported in the cov field of the output file. If this parameter is not used, then the sum of the coverage of each unioned transcript (i.e., sum up of the coverage of all transcripts in the input gtf files that are identical to this transcript) will be recorded and reported in the cov field of the output file.

gtfcuff

This tool is to evaluate the accuracy of predicted transcripts. To use this tool, you first need to run gffcompare, which will generate several files, and among them gtfcuff will usually use .tmap. For example, to compute the AUC score (the parameter used to draw the curve is the predicted coverage of all the transcripts), you can use

gtfcuff auc <gffcompare.tmap> <number-of-exons-in-reference>

The last parameter is usually the number of multi-exon transcripts in the reference annotation. You can find this number in the .stats file produced by gffcompare. The AUC score will be printed to the standard output.

gtfformat

This tool is to process single gtf file. It provides several functions. First, you can use the following command to only select those transcripts whose length are in the range between min-length and max-length. Note that here length is defined as the sum of the lengths of all exons in the transcript.

gtfformat <min-length> <max-length> <input-gtf-file> <output-gtf-file>