Hi,
New to working with Illumina data. I am running into some inconsistency issues on what programs will recognize my file. For example, bowtie works just fine with the file, however, Galaxy, the FastX Toolkit and Stampy all give me error messages in regards to line 4 containing the quality information. I have read lots of posts about converting to Sanger, the variety of Illumina generated FastQ formats, but have yet to completely identify the issue. Some of the data is below.
Any thoughts or recommendations?
@HWUSI-EAS-100R_0003:8:1:1034:19859#NCCCCC/1
GGTATGTTAACATTCANTGAGCTATACACTTAAGATTTGTGCACTTTATCATAGTAAGTTATTTGTCAGTTTGAA
+
ddadcdeeeedddd^bBa]\ZX[^Xdddaddca^a\dddab^J]`[Y^`^^cLa^c`a`YJWOSSRb\_BBBBBBB
@HWUSI-EAS-100R_0003:8:1:1034:9367#NCCCTC/1
CACTGAATGACATGGGACTGTTTGGACAAAACGTGCTATACCTCTACCTCGGGAGGGCCGGTTACACCATACATG
+
eceeeeedefcdfcfdcc^a`c^_`_Y^^\M^][^baYa\a^K^^T[]Y^BBBBBBBBBBBBBBBBBBBBBBBBBB
@HWUSI-EAS-100R_0003:8:1:1035:9515#NCTATG/1
CGCCGTTTCCCAGTAGGTCTCCTAGAACACTATTTCAATGATGAACAAGGCGAGATCGAGCTCATTGAGACCTCG
+
feefffffdfffedcdcbe\bdaa^T^^YaT^_\Sa^\^^YY^^^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
EDIT: Just noticed that there are 75 bp and 76 ascii quality scores. Am I missing something here?
Many thanks,
Scott
New to working with Illumina data. I am running into some inconsistency issues on what programs will recognize my file. For example, bowtie works just fine with the file, however, Galaxy, the FastX Toolkit and Stampy all give me error messages in regards to line 4 containing the quality information. I have read lots of posts about converting to Sanger, the variety of Illumina generated FastQ formats, but have yet to completely identify the issue. Some of the data is below.
Any thoughts or recommendations?
@HWUSI-EAS-100R_0003:8:1:1034:19859#NCCCCC/1
GGTATGTTAACATTCANTGAGCTATACACTTAAGATTTGTGCACTTTATCATAGTAAGTTATTTGTCAGTTTGAA
+
ddadcdeeeedddd^bBa]\ZX[^Xdddaddca^a\dddab^J]`[Y^`^^cLa^c`a`YJWOSSRb\_BBBBBBB
@HWUSI-EAS-100R_0003:8:1:1034:9367#NCCCTC/1
CACTGAATGACATGGGACTGTTTGGACAAAACGTGCTATACCTCTACCTCGGGAGGGCCGGTTACACCATACATG
+
eceeeeedefcdfcfdcc^a`c^_`_Y^^\M^][^baYa\a^K^^T[]Y^BBBBBBBBBBBBBBBBBBBBBBBBBB
@HWUSI-EAS-100R_0003:8:1:1035:9515#NCTATG/1
CGCCGTTTCCCAGTAGGTCTCCTAGAACACTATTTCAATGATGAACAAGGCGAGATCGAGCTCATTGAGACCTCG
+
feefffffdfffedcdcbe\bdaa^T^^YaT^_\Sa^\^^YY^^^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
EDIT: Just noticed that there are 75 bp and 76 ascii quality scores. Am I missing something here?
Many thanks,
Scott
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