This is my first time analyzing bisulfite sequencing. I've downloaded this ENCODE whole genome bisulfite sequencing data to analyze using Bismark. I can't find anywhere on that page where it clearly says whether it's stranded or not. I did a test alignment with one of the files (ENCFF001ZVL) of 1 million reads and these are the results:
Default (strand-specific) alignment:
--non_directional (non-strand specific) alignment:
Default (strand-specific) alignment:
Code:
Final Alignment report ====================== Sequences analysed in total: 1000000 Number of alignments with a unique best hit from the different alignments: 786594 Mapping efficiency: 78.7% Sequences with no alignments under any condition: 115586 Sequences did not map uniquely: 97820 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 394999 ((converted) top strand) CT/GA: 391595 ((converted) bottom strand) GA/CT: 0 (complementary to (converted) top strand) GA/GA: 0 (complementary to (converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
Code:
Final Alignment report ====================== Sequences analysed in total: 1000000 Number of alignments with a unique best hit from the different alignments: 785277 Mapping efficiency: 78.5% Sequences with no alignments under any condition: 114820 Sequences did not map uniquely: 99903 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 394212 ((converted) top strand) CT/GA: 390840 ((converted) bottom strand) GA/CT: 116 (complementary to (converted) top strand) GA/GA: 109 (complementary to (converted) bottom strand)
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