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
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
![Smile](https://www.seqanswers.com/core/images/smilies/smile.png)
------------------ <-------------
--------->-----------------------
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
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