pair orientation

[lpantano]

Hi,

I am using this tool to test some data, and I see that there you allow inward and outward pair orientation. Any chance to have an option to filter that?

thanks!

[zyndagj]

Hello,

There already is a --pair option that only processes properly paired mappings that corresponds to the -n option you use with the main bsmap program. Does that fit your needs?

Thanks,
Greg

[lpantano]

Thanks for the answer. I already use that. But when I do samtools stats after filtering the reads by proper paired, I get these pair orientation stats. I don’t know exactly how samtools stats is counting reads in inward or outward orientation, or if you are using that bit to code another thing that actually is not related to inward/outward orientation? like here: https://github.com/zyndagj/BSMAP/blob/master/README.txt#L142

If you tell me that using —pair is only using reads that are proper paired, meaning inward orientation, i am fine with that, and will ignore samtools stats in this case.

thanks a lot!

On Apr 18, 2016, at 3:38 PM, Greg Zynda notifications@github.com wrote:

Hello,

There already is a --pair option that only processes properly paired mappings that corresponds to the -n option you use with the main bsmap program. Does that fit your needs?

Thanks,
Greg

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You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub #2 (comment)

[zyndagj]

I would have to dig into the code to see what it is doing, but the --pair
flag is definitely a filter step, separate from the alignment, and will
only use reads with the 0x2 flag. If you use the default -n 0, the 0x2
flag should only be assigned to inward-facing reads (FR). Most illumina
pairwise sequencing is done in this fashion. You can force the use of these
reads with the --pair flag as I mentioned above. If you really want to
use outward-facing reads (RF, usually from mate-pair libraries), I believe
you'll need to use the -n 1 Cokus protocol and then filter your bam file
with the appropriate flags. Be sure to not use the --pair with your
hand-filtered file unless you are also editing the 0x2 flag.

You can also check to see what kind of data you have with something like
http://rseqc.sourceforge.net/#infer-experiment-py after running with the
cokus protocol.

On Mon, Apr 18, 2016 at 3:17 PM, Lorena Pantano notifications@github.com
wrote:

Thanks for the answer. I already use that. But when I do samtools stats
after filtering the reads by proper paired, I get these pair orientation
stats. I don’t know exactly how samtools stats is counting reads in inward
or outward orientation, or if you are using that bit to code another thing
that actually is not related to inward/outward orientation? like here:
https://github.com/zyndagj/BSMAP/blob/master/README.txt#L142

If you tell me that using —pair is only using reads that are proper
paired, meaning inward orientation, i am fine with that, and will ignore
samtools stats in this case.

thanks a lot!

On Apr 18, 2016, at 3:38 PM, Greg Zynda notifications@github.com
wrote:

Hello,

There already is a --pair option that only processes properly paired
mappings that corresponds to the -n option you use with the main bsmap
program. Does that fit your needs?

Thanks,
Greg

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You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub <
https://github.com/zyndagj/BSMAP/issues/2#issuecomment-211543882>

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You are receiving this because you commented.
Reply to this email directly or view it on GitHub
#2 (comment)

[lpantano]

that's perfect, I want only inward oriented reads, so I am happy just using --pair option.

thanks a lot for the support. I was a little scared to be seeing the outward orientation having a high percentage of reads (1/3) the total. I will try to give you a toy example of this in case it could help someway.

thanks