Dear All,
I'm using fastx toolkit to remove reads with unkown bases however I'm getting an error for "invalid nucleotide sequence".
Here's part of the fastq file
@HWI-ST261:1:1:1470:2174#CGATGT/1
TGAAACTG.G.TTT.C.................................C
+
__`__BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-ST261:1:1:1408:2220#CGATGT/1
GCCAGTCA.AAGTTGAGGCAGCTTCAAAAGATGGTCCATGATATTAAAAA
+
gggggcddBdccaccfggggggggggggggYcffagggegebaggggcdg
@HWI-ST261:1:1:1449:2221#CGATGT/1
GCGACTTT.ACCGAGAGGCTGCTGGAGCTCGTGTTTGGACGCGATGTTTC
+
bbbbbbbbBb`aab^bbbbb`QQV^BBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-ST261:1:1:1385:2244#CGATGT/1
AATAATCTCTGTCTTTCAGAAGCCCCAGGTTGATCTTGAATTAAATAACA
+
dggggggggggdggggggggggggggggecceddgeeggeebgedggddg
@HWI-ST261:1:1:1648:2175#CGATGT/1
ATCTGTTT.T.TTG.C.................................T
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
I'm assumiong the a "." is an unkown base. Is there a efficient script I can use to change the "." to N's?
I'm using fastx toolkit to remove reads with unkown bases however I'm getting an error for "invalid nucleotide sequence".
Here's part of the fastq file
@HWI-ST261:1:1:1470:2174#CGATGT/1
TGAAACTG.G.TTT.C.................................C
+
__`__BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-ST261:1:1:1408:2220#CGATGT/1
GCCAGTCA.AAGTTGAGGCAGCTTCAAAAGATGGTCCATGATATTAAAAA
+
gggggcddBdccaccfggggggggggggggYcffagggegebaggggcdg
@HWI-ST261:1:1:1449:2221#CGATGT/1
GCGACTTT.ACCGAGAGGCTGCTGGAGCTCGTGTTTGGACGCGATGTTTC
+
bbbbbbbbBb`aab^bbbbb`QQV^BBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-ST261:1:1:1385:2244#CGATGT/1
AATAATCTCTGTCTTTCAGAAGCCCCAGGTTGATCTTGAATTAAATAACA
+
dggggggggggdggggggggggggggggecceddgeeggeebgedggddg
@HWI-ST261:1:1:1648:2175#CGATGT/1
ATCTGTTT.T.TTG.C.................................T
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
I'm assumiong the a "." is an unkown base. Is there a efficient script I can use to change the "." to N's?
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