Comments (6)
dpryan79
commented on June 23, 2024
Sure, please send the dropbox link to redacted.
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dpryan79
commented on June 23, 2024
You have a couple issues going on. Firstly, your MAPQs are all below the default threshold, so you'll need to change that (the -q option). Secondly, all of your Cs are on the bottom strand, but you have almost no fragments originating from that strand (unless these were PBAT and the strand information didn't get fixed). Finally, you'll need to change the maximum depth option (-D) to something like 10000000, since almost all of your alignments are stacked on top of each other.
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antoine4ucsd
commented on June 23, 2024
thanks for taking the time to look at it! Very much appreciated ++
I will give it a try with your suggested parameters and on other samples. I will keep you informed about how it works.
Best,
… On Oct 5, 2017, at 7:12 AM, Devon Ryan ***@***.*** ***@***.***>> wrote:
You have a couple issues going on. Firstly, your MAPQs are all below the default threshold, so you'll need to change that (the -q option). Secondly, all of your Cs are on the bottom strand, but you have almost no fragments originating from that strand (unless these were PBAT and the strand information didn't get fixed). Finally, you'll need to change the maximum depth option (-D to something like 10000000), since almost all of your alignments are stacked on top of each other.
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dpryan79
commented on June 23, 2024
Happy to help, keep in mind that without changing the strand information you'll still have low depth. Not knowing exactly how the experiment was performed I don't know if the inferred strand is really correct.
Also, make sure to use --CHH :)
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antoine4ucsd
commented on June 23, 2024
Got it!
… On Oct 5, 2017, at 7:20 AM, Devon Ryan ***@***.***> wrote:
Happy to help, keep in mind that without changing the strand information you'll still have low depth. Not knowing exactly how the experiment was performed I don't know if the inferred strand is really correct.
Also, make sure to use --CHH :)
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antoine4ucsd
commented on June 23, 2024
thank you again!
It did work. I will try to improve the sequencing upfront but this is promising
Best,
a
… On Oct 6, 2017, at 7:07 AM, Devon Ryan ***@***.*** ***@***.***>> wrote:
Closed #53 <#53>.
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Related Issues (20)
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