extracts sequences and quality scores from FASTQSOLEXA data
fastqsolexa_to_fasta_qual.py $input1 $output1 $output2 $input1.extension
.. class:: warningmark
IMPORTANT: This tool currently only supports data where the quality scores are integers or ASCII quality scores with base 64.
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**What it does**
This tool extracts sequences and quality scores from FASTQ data ( Solexa variant ), producing a FASTA dataset and a QUAL dataset.
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**Example1**
- Converting the following Solexa fastq data::
@seq1
GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
+seq1
hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh
@seq2
GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
+seq2
hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO
- will extract the following sequences::
>seq1
GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
>seq2
GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
- and quality scores::
>seq1
40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 0 40 40 40 40 40 40
>seq2
40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 33 40 40 40 40 23 40 1 40 6 40 19 9 10 7 3 40 15
**Example2**
- Converting the following Solexa fastq data::
@HANNIBAL_1_FC302VTAAXX:2:1:228:167
GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
+HANNIBAL_1_FC302VTAAXX:2:1:228:167
40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
@HANNIBAL_1_FC302VTAAXX:2:1:156:340
GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
+HANNIBAL_1_FC302VTAAXX:2:1:156:340
40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9
- will extract the following sequences::
>HANNIBAL_1_FC302VTAAXX:2:1:228:167
GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
>HANNIBAL_1_FC302VTAAXX:2:1:156:340
GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
- and quality scores::
>HANNIBAL_1_FC302VTAAXX:2:1:228:167
40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
>HANNIBAL_1_FC302VTAAXX:2:1:156:340
40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9