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qseq2fastq converst Illumina Deep Sequencing Qseq files to more commonly used FastQ format.
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ahcm/qseq2fastq
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* ABOUT qseq2fastq qseq2fastq converst Illumina Deep Sequencing Qseq files to more commonly used FastQ format. This is mostly a transformation of selected columns of the Qseq file. The Phred score is also transformed. Without -a option reads the sequencer marks a bad are filtered out. Usually I would recommend using -a and handling the quality later in the pipeline. It is implemented in C for speed. Written and designed by Andreas Hauser <[email protected]>, <[email protected]>. It was initially based on qseq2fastq.pl: http:https://sourceforge.net/projects/qseq2fastq/ * INSTALLATION ** DOWNLOAD http:https://www.splashground.de/software/qseq2fastq-andy/qseq2fastq-andy-3.0.tar.gz ** COMPILE $ make Note Linux x86_64 (Scientific Linux 6) is already containedprecompiled. ** INSTALL $ make install INSTALL_PREFIX=/usr/local where /usr/local is the path where the binary will be installed in the subfolder bin, e.g. /usr/local/bin in this case. * BUGS Please do report them to Andreas Hauser <[email protected]> or github: https://github.com/ahcm/qseq2fastq/issues * USAGE $ qseq2fastq -a s_1_1_*_qseq.txt > s_1_1.fastq But in addition it can now do multiplexing. As you can see this much more complex. E.g. $ qseq2fastq -a -b ACTTGAA,GCCAATA,TGACCAA,ACAGTGA,CAGATCA -o out/s_1_1_0010_ -d s_1_2_0010_qseq.txt s_1_1_0010_qseq.txt > out/s_1_1_0010_MISMATCH.fastq Where -b gives the barcodes (the ones in the barcode lane, so be careful about inversion from your adapter sequences etc.) -d gives the qseq file with the barcode reads -o gives the prefix for the output files (one for each barcode). If the output files exist output will be appended. The prefix can like above contain a directory but that directory must exist. The reads without a matching barcode are written to standard out so they can either be discarded (> /dev/null) or like above be written to file (out/s_1_1_0010_MISMATCH.fastq). It's easy to convert a tile like this as each tile has its own file. To convert a whole lane one can either concatenate the files: $ cat s_1_1_*_qseq.txt > s_1_1.qseq $ cat s_1_2_*_qseq.txt > s_1_2.qseq Since the star is usually expanded in alphabetical order (by your shell (e.g. zsh) so be careful if you don't use such a shell) this will preserve the order and the lines in the both files will correspond. Another way is to use a loop and the appending feature of qseq2fastq. $ for i in `seq -w 1 120`; do qseq2fastq -a -b ACTTGAA,GCCAATA,TGACCAA,ACAGTGA,CAGATCA -o out/s_1_1_ -d s_1_2_0${i}_qseq.txt s_1_1_0${i}_qseq.txt >> out/s_1_1_MISMATCH.fastq; done
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