Keren Zhou

> To clarify, you would need a `--extendReads INT` that will artificially count the read coverage from the read starting base to INT base downstream? This option will artificially count...

> As an experimental feature, I added `--extendRead INT` in bamtocov today, that will artificially set the end of an alignment at (alignment start + INT) nucleotides (or the end...

> Is this related to #6, and specifically, are you interested in read counts (counting the number of reads mapped) in both issues rather than nucleotide coverage? Hi telatin, these...

> Ok, consider that `bamtocov` computes nucleotide coverage, while `bamtocounts` focuses on read counts on a target, and it has some options for normalization already built-in. Oh, I must misunderstand...

> It is really strange that MACS found the average insertion size over 10k from both treatment and control. Do you mind share with me part of the bam file...

I tried run `intervene venn --bedtools-options s`, but it returned the same result with that without `--bedtools-options s`.

> You should use `enricher()`, see https://yulab-smu.top/biomedical-knowledge-mining-book/universal-api.html#msigdb-analysis Thank you! I've tried enricher() and works fine! Best, Keren

Hi Jens, Thanks for your reply. What puzzles me is about the expected endpoints. Could you please explain more about it? Best, Keren

> If I understand the question correctly, in this case AA identified a segment of the genome (which was presumably amplified, though I cannot tell without seeing the estimated CN)....

Thank you so much, Jens! Stay safe during this challenging time! Best, Keren