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  • Is this bisulfite sequencing stranded or not?

    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:

    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
    --non_directional (non-strand specific) alignment:

    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)

  • #2
    You can go by those results and declare it to be strand-specific. In my experience, at least, that's more common than unstranded datasets too.

    Comment

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