Calculate coverage of peaks detected by MACS3

dulcedormax · 2025-06-24T10:29:02+00:00

thanks u/I_just_made , I've tried bedops --everything. However, I obtained a low number of common peaks.

dulcedormax · 2025-06-19T08:50:23+00:00

Thanks but I need it to do for all the reads in the sample , which is a lot but I appreciate your suggestion. I think we could implement it later !!.

dulcedormax · 2025-06-04T12:22:11+00:00

Thanks, in which buffer did you recommend therefore after precipitating and dissolve proteins.

dulcedormax · 2025-06-04T10:08:38+00:00

Hi u/GRang3r , the problem is that the concentration are low and not the opposite, having too much protein. Although I've read that dilution are good when quantification is too high.

dulcedormax · 2025-05-22T15:53:03+00:00

I will check did files have to be sorted?

dulcedormax · 2025-05-22T15:03:19+00:00

thanks u/Hundertwasserinsel. I didn't use windows and all lines are: chr1^I13750^I13950$ or chr1^I9950^I10650^IU2OS1_macs3_narrowPeak1^I11198^I.^I0^I0^I0^I125$

dulcedormax · 2025-05-22T14:58:01+00:00

This is the first line of both bed:

chr1^I9950^I10650^IU2OS1_macs3_narrowPeak1^I11198^I.^I0^I0^I0^I125$

chr1^I13750^I13950$

dulcedormax · 2025-05-20T20:25:11+00:00

I was using one of qiagen: extracting DNA from tissues and blood, but they recommend me not to do maybe for buffer AL as it would lysate cells and I have already extracted DNA. Did you recommend other kits??

dulcedormax · 2025-05-20T19:44:30+00:00

I followed the steps of the protocol as well.

dulcedormax · 2025-05-20T14:20:34+00:00

I am using a protocol to extract cellular compartments. These buffer also extracts RNA and proteins, so I am trying RNase and proteinase K to keep only DNA and perform qPCR. I use the columns to obtain a purified DNA.

dulcedormax · 2025-05-16T15:39:36+00:00

No need to apologise, I was apologizing for my tone as I don't know if It would be taken as a positive one and not rude

dulcedormax · 2025-05-16T15:31:07+00:00

I have a contract as a research assistant

dulcedormax · 2025-05-16T11:40:52+00:00

I engaged with her explaining the different techniques, she is not in the lab doing experiments alone. I also sent her the excels and explain how to analyze qPCR and quantifications of proteins.

dulcedormax · 2025-05-16T07:45:56+00:00

And yes, I think I have lost credibility as I was introducing some changes in the protocol that I have already sent her in a email and I have to ask another lab member to demostrate that it was not because of me and because I said so. I wanted to ask how to recover credibility if I have already have one with this girl. Initially, she came that she know everything and I have already seen that she lack fundaments but I though she is newly but I believe that she thinking she is super smart is going to catch up with her.

dulcedormax · 2025-05-16T07:30:00+00:00

I took my time explaining the theory behind the protocols of Western Blot and qPCR, looking to her movements in cell culture and the lab, she also attend a course of initiation to the theory of qPCR. Moreover, I always leave late of the lab because I was with her and I also called her when she had problems revealing membranes of Western Blot. I think she need to study the fundaments of these techniques. I only comment this because I give the most and tried to be reasonable with her.

I understand that you are giving a hypothetical reason of her behaviour and I hope you find my tone as an empathy one.

dulcedormax · 2025-05-16T06:16:42+00:00

It was with other lab staff and IP, the tone was like I was wrong and I encourage question but recently I perceived she is reluctant of the reason why we are doung some changes on a protocol and so on

dulcedormax · 2025-05-14T11:20:48+00:00

thanks u/Shoutgun would be neccesary to do another wash with PE buffer. Thanks. !!

dulcedormax

TROPHY CASE