Sorry for the very basic question. I am dealing with "raw" Illumina data for the first time and I am not sure how to pre-process the reads.
The *sequence.txt file for each lane contains reads that have tons of 'N' at the end, with quality 'B'. (see below)
How can I tell if this is normal or if something went wrong with the sequencing run?
For example:
@HWI-EAS413_0021:2:1:1159:4065#0/1
TCGTGCCCGGGTAGCTCTGACTGGGCTGACTGTGGCTGAATACTTNAGNGACNANGAAGGTCANGAGATCGG
+HWI-EAS413_0021:2:1:1159:4065#0/1
dddb\dddcd^aaccdcdd\cdd^dadddc^c`ccdcd`d^`b``B\ZB`UYB]BUUU^][]_B_VWWWYT^
@HWI-EAS413_0021:2:1:1159:11764#0/1
GTGTGCCTGGTCATGCTGTGGTGGATCACCGTCCCAGGGCATTGGNGANTTNNGNATTTACGANATCGGAAG
+HWI-EAS413_0021:2:1:1159:11764#0/1
fffefffffffffeffffdff_ffefffffffeff`eedd`a^b`B\VB`]BB]B_aa\^_`_BaO[[Y]dc
The *sequence.txt file for each lane contains reads that have tons of 'N' at the end, with quality 'B'. (see below)
How can I tell if this is normal or if something went wrong with the sequencing run?
For example:
@HWI-EAS413_0021:2:1:1159:4065#0/1
TCGTGCCCGGGTAGCTCTGACTGGGCTGACTGTGGCTGAATACTTNAGNGACNANGAAGGTCANGAGATCGG
+HWI-EAS413_0021:2:1:1159:4065#0/1
dddb\dddcd^aaccdcdd\cdd^dadddc^c`ccdcd`d^`b``B\ZB`UYB]BUUU^][]_B_VWWWYT^
@HWI-EAS413_0021:2:1:1159:11764#0/1
GTGTGCCTGGTCATGCTGTGGTGGATCACCGTCCCAGGGCATTGGNGANTTNNGNATTTACGANATCGGAAG
+HWI-EAS413_0021:2:1:1159:11764#0/1
fffefffffffffeffffdff_ffefffffffeff`eedd`a^b`B\VB`]BB]B_aa\^_`_BaO[[Y]dc
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