We have some illumina 1.5/phred64 files that we need to process. We used Trimmomatic's tophred33 option to convert to phred33 encoding (the idea being to do all downstream analysis in phred33). But after then running through bfc, some of the reads were converted back to phred64. Here is an example. The conversion back to phred64 happens in the reads that get "ec:Z:3" added to the info line.
Hi,
We have some illumina 1.5/phred64 files that we need to process. We used Trimmomatic's tophred33 option to convert to phred33 encoding (the idea being to do all downstream analysis in phred33). But after then running through bfc, some of the reads were converted back to phred64. Here is an example. The conversion back to phred64 happens in the reads that get "ec:Z:3" added to the info line.
original read
@FCC3PRVACXX:5:1101:5113:1970#AGCGCTAG/1 NACACCGGCACCCTTAAAATTCTACGGTATCGATTTCGGAGACAGCAGACTTTTGGAATTATACGTATTCCGTTTATATGTGTTCTGTAAGCAGTTTTAT + BPaceeeegggggiiiihiiiiiiiiiegiiifhiiiiihifghiiiihigggggeeeeedddddbdccedcbcccccedcceccdcddcbcccccdccc
post trimmomatic -tophred33, and leading N also trimmed
@FCC3PRVACXX:5:1101:5113:1970#AGCGCTAG/1 ACACCGGCACCCTTAAAATTCTACGGTATCGATTTCGGAGACAGCAGACTTTTGGAATTATACGTATTCCGTTTATATGTGTTCTGTAAGCAGTTTTAT + 1BDFFFFHHHHHJJJJIJJJJJJJJJFHJJJGIJJJJJIJGHIJJJJIJHHHHHFFFFFEEEEECEDDFEDCDDDDDFEDDFDDEDEEDCDDDDDEDDD
post bfc
@FCC3PRVACXX:5:1101:5113:1970#AGCGCTAG/1 ec:Z:3 ACACCGGCACCCTTAAAATTCTACGGTATCGATTTCGGAGACAGCAGACTTTTGGAATTATACGTATTCCGTTTATATGTGTTCTGTAAGCAGTTTTAT + Paceeeegggggiiiihiiiiiiiiiegiiifhiiiiihifghiiiihigggggeeeeedddddbdccedcbcccccedcceccdcddcbcccccdccc