BFAST question/problem

[kenietz]

Hi guys,
i have the following question about BFAST postprocess: What command one must issue to postprocess SOLID PE data? In the manual is a bit obscure:
-------------------------------------------------
-S INT, --strandedness=INT
Specifies the pairing strandedness: The option -S 0 specifies that the reads
should be mapped onto the same strand. The option -S 1 specifies that the
reads should be mapped onto the opposite strand.

-P INT, --positioning=INT
Specifies the pairing positioning: The option -S 0 specifies that the first read
should be (5’) upstream of the second read (sequencing strand). The option
-S 1 specifies that the second read should be (5’) upstream of the first read
(sequencing strand). The option -S 2 specifies that there is no positioning.

-Y INT, --pairing=INT
Specifies the pairing orientation: The option -S 0 specifies that the reads are
paired ends (-S 0 -P 1). The option -S 1 specifies that the reads are mate pairs
(-S 1 -P 0). The option -S 2 specifies that no pairing should be performed.
--------------------------------------------------------

It seems that the manual is a bit messed up From what i found SOLID PE reads are oriented like this:

------------------ <-------------
--------->-----------------------

I tried with -Y 0 but then i got no properly paired reads. So im not sure if -Y 0 is the proper argument as it is corresponding to -S 0 (same strand) -P 1 (second read should be (5’) upstream of the first read).

Can you please help me with that problem?
Thank you in advance

[nilshomer]

I wrote it down once here: http://sourceforge.net/apps/mediawik...aired_End_Mode

I am quoting below:

Paired end reads have the following orientation:

5' E1 -----> ....             3'
3'           .... <------- E2 5'

Above, the start co-ordinate of E1 is less than E2, with E1 and E2 reported on opposite strands.

Mate pair reads have following orientation

5' E2 -----> .... E1 -------> 3'
3'           ....             5'

Above, the start co-ordinate of E1 is greater than E2, with E1 and E2 reported on the same strand.

So for SOLiD mate pair reads, the R3 tag (E2) is listed before the F3 tag (E1). For SOLiD paired end reads, the F3 tag (E1) is listed before the F5 tag (E2).

[kenietz]

Thanks a lot Nils

[kenietz]

Hi Nils,
just to add that then the manual is wrong. There is said that for paired end one must use -S 0 and -P 1 (-Y 0) but in fact one must use -S 1 and -P 0 (-Y 1).

[nilshomer]

Hi Nils,
just to add that then the manual is wrong. There is said that for paired end one must use -S 0 and -P 1 (-Y 0) but in fact one must use -S 1 and -P 0 (-Y 1).

It looks like something is wrong here. Can someone confirm my interpretation of paired ends and mate pairs? If paired ends are mapped on the opposite strand, then the BFAST manual is wrong .