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Recent Replies
Answer: Building database with snpEff -- -gtf22 option not recognized/file not read
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michael.dhar
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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
samtools view -h x.bam | grep MM
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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
Then use something like
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> is this normal to receive the bam files in this shape and
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Thank you for your reply!
Although I don't really understand how to use hard Threshold.
I plotted raw correlations and kept the most correl…
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