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Comment: normalize between 2 different platform
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1364454115
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Hello,
Could you please tell me whether different datesets generated by multiplex PCR and 5'UMI-tagged 5′-RACE can be analyzed together? T…
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gynecoloji
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Thanks for your response.
I think it may be better to keep those repetitive regions and only filter out the blacklisted regions.
This is a …
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IDR addresses a different problem than removal of reads aligning to blacklist reads, though it's unquestionably useful for deriving more ro…
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Simply posting a snippet of error message in a question is the reason you have not received any responses.
Please make an effort to formu…
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Based on the ordering of the commands here: https://github.com/pcingola/SnpEff/issues/583
I believe I just needed to place the "build" c…
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ATS
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That's great to know. Thanks for your input!
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It should be noted that concerns about mapping artifacts in ChIP-seq really come from an era where reads were 36bp (or even 25bp!) in lengt…
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AGain you seem to be over-filtering. Your mean.k and median.k are really low, so I think the number of input genes you used for this is ver…
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I am going to guess you've seen/thoroughly read [this paper about the ENCODE blacklist regions](https://www.nature.com/articles/s41598-019-…
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When you have a bam make sure you check the methyl tags MM and ML are present. Something like
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yes keeping both mapping info and methylation info at the same time is the intention. Thanks so much for the reosponse! I will try it
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> OP wants to align AND keep the methylation info
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> is this normal to receive the bam files in this shape and
Yes. If you asked for methylation calls then this is a way to capture that i…
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