TrimSequencesTo.pl - Trims all nucleotide sequences at the 3'-end to a given length
# Minimal argument call, specifying all required parameters.
TrimSequencesTo.pl --input fastafile.fa --output trimmedsequences.fa
# Maximal argument call, specifying all possible parameters.
TrimSequencesTo.pl --input fastafile.fa --output trimmedsequences.fa
--trimto 32
The input file. Has to be a multiple fasta file. Mandatory parameter
The output file. Mandatory parameter
The length to which the nucleotide sequences should be trimmed. default=32
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The script trims each nucleotide sequence of a multiple fasta file at the 3'-end to a given length. Shorter sequences will be left unaltered. Solexa reads usually accumulate mismatches at their 3'-ends which may impede mapping of the reads. The script may thus be useful, for example, to trim all no-matches of a mapping step to 22 bp and repeat the mapping with this trimmed no-matches.
Multiple fasta files. For example:
>43||Count=1 GAAATTTAAGAAACAATTATAATCCAC >44||Count=1 ATTCGCGTTCAGCTGAGGCAGAGTGATGGT >45||Count=2 TCCCTGTGGTCTATTGTTTATGATTCGGCT >46||Count=1 TCCCGGGGCGTCTAGTGGTTAGGGTTTGGCG >47||Count=3 TTCCTGTTGTCTAGTGGTTAGG
A multiple fasta file, containing the trimmed sequences. For example, the sequences shown above trimmed to 22 nt:
>43||Count=1 GAAATTTAAGAAACAATTATAA >44||Count=1 ATTCGCGTTCAGCTGAGGCAGA >45||Count=2 TCCCTGTGGTCTATTGTTTATG >46||Count=1 TCCCGGGGCGTCTAGTGGTTAG >47||Count=3 TTCCTGTTGTCTAGTGGTTAGG
Perl 5.8 or higher
Robert Kofler
Heinz Himmelbauer
robert.kofler at crg.es