cutleraging
cutleraging
Hi Mousumy, In R, I checked if my mutations overlapped the regions in the bed file as follows ``` > vcf.obs vcf.obs bed seqlevelsStyle(bed) length(unique(queryHits(overlaps.obs))) == length(vcf.obs) [1] FALSE ```...
Hi @MousumyCSE , Files are here: https://www.dropbox.com/scl/fo/tva1jkwd5iainmz7c2l7n/h?rlkey=luw0vxidbvghglu0oojgucdm5&dl=0 Thanks for taking a look! Ronnie
Thank you Johannes for you reply. I have done something similar with what you suggested with some test data, but now am trying to load my actual data using the...
Hi all, Any help on this? Thanks, Ronnie
Hi Vadim, Thanks for the helpful response. I am now trying this out. Let say I have a certain histone peptide that has 2 sites which can be modified. Do...
Hi Vadim, Thanks for the response, I will try that out. That's surprising that a spectral library can be built better with DIA than DDA. Are there any further recommendations...
Hi Vadim, Thanks for the replies. In regards to the modifications, the +56.026215 is actually a fixed mod and like a label. Meaning that it will be on every peptide....
Okay got it. However, I see that PTMs can also get a Q-value using --ptm-qvalues. Is this relevant here, especially since my spectral library contains many and diverse modifcations?
Hi Vadim, I tried to implement your advice to improve the searches. My samples are whole cell lysate so there is a good amount of background. Here is what I...
Oh I see now, they are only a couple of MB. Thanks. Only can know the size if I look at the properties of each folder. Is there a way...