T-lex does not work and I got error messages, what should I check?
1- Check that all the requirement are there (e.g. program installed, good version of the program)
2- Check the input data:
a) The sequencing data (fastq files) have to be stored in a folder and a sub-folder such as: folder -> subfolder -> X_read1.fastq.
b) The format of the fastq files has to be STANDARD (see http://en.wikipedia.org/wiki/FASTQ_format). Use the script fq_allstd.pl part of the MAQ package. the command line is: fq_allstd.pl sol2std [raw fastq file] > [standard fastq file].
c) The TE names should not contain any special characters (e.g., "~`!@#$%^&*()_-+=").
d) The name of the TE should be short, less than 15 characters.
e) The chromosome and TE names have to correspond in the input files.
Last edit: Anna-Sophie Fiston-Lavier 2013-04-19
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
T-lex does not work and I got error messages, what should I check?
1- Check that all the requirement are there (e.g. program installed, good version of the program)
2- Check the input data:
a) The sequencing data (fastq files) have to be stored in a folder and a sub-folder such as: folder -> subfolder -> X_read1.fastq.
b) The format of the fastq files has to be STANDARD (see http://en.wikipedia.org/wiki/FASTQ_format). Use the script fq_allstd.pl part of the MAQ package. the command line is: fq_allstd.pl sol2std [raw fastq file] > [standard fastq file].
c) The TE names should not contain any special characters (e.g., "~`!@#$%^&*()_-+=").
d) The name of the TE should be short, less than 15 characters.
e) The chromosome and TE names have to correspond in the input files.
Last edit: Anna-Sophie Fiston-Lavier 2013-04-19