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Old 08-30-2015, 09:04 PM   #1
biocomputer
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Location: Canada

Join Date: Dec 2013
Posts: 62
Default 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)
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Old 08-31-2015, 10:16 AM   #2
dpryan
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Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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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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