countTags - counting a set of k-mers into a set of FASTQ files

Installation

1. Clone this repository : git clone --recursive https://gitlab:get/counttags.git or git clone https://gitlab:get/counttags.git && git submodule init && git submodule update
2. Compile the software : make
3. Place the binary somewhere acessible in your $PATH

Usage

First you need to create a file containing the tags you want to quantify. You can use three tags format:

• fasta format
• separator format : sequence name (the separator can be a space or a tabulation or a comma or a semi-comma)
• raw format : only the tag sequence

You must use option '-i' to specify the tag file. You can provide the tags file via the standard input by using '-i -' as filename. If you file is gziped, you can pass directly to the '-i mytags.gz' option or the pipe if needed, but if it is in other compression format, uncompress the file with the right tool and pass to countTags via the pipe and option '-i -'.

All tags must have at least the K-mer length, if too short, tags are discarded. The maximum authorize tag length is 32bp.

K-mer length must be provided to countTags using the -k INT option.

For example :

countTags -k 31 file.fa file1.fastq.gz file2.fastq.gz

Managing stranded files

By default, countTags count the canonical tag between the forward and the reverse tag (the first one in alphabeticl order) and output this sequence in the result.

If you want only one strand to be count, you have to provide the tag sequence in the strand that you want to count and use the option '--stranded' for countTags. Therefore, for stranded paired fastq files you will count only one pair, the one in the same strand that your tag. For paired fastq see below the '--paired' option.

Managing Paired-End files

You can now use the '--paired format' option to count stranded pair-end fastq file. You have to specify the pair-end format: either 'rf' (the most used), 'fr' or 'rr' in accordance with the library setup. In this case, only the two paired fastq file must be given.

When you set the paired option, the stranded option is set to true, otherwise this is meaning nothing.

For paired-end files, you can use the '--merge-counts' option to get the total count for the sample.