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-   -   Is this bisulfite sequencing stranded or not? (http://seqanswers.com/forums/showthread.php?t=62340)

biocomputer 08-30-2015 09:04 PM

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)


dpryan 08-31-2015 10:16 AM

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.


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