User: sergio.espeso-gil

Reputation:
0
Status:
New User
Location:
New York
Last seen:
1 year, 4 months ago
Joined:
4 years, 1 month ago
Email:
s************@crg.eu

Post-doctoral Fellow

Icahn School of Medicine at Mount Sinai

 


 

Posts by sergio.espeso-gil

<prev • 54 results • page 1 of 6 • next >
0
votes
2
answers
432
views
2
answers
Answer: A: Extracting non-interacting hic reads to create a sam/bam file
... Thanks! That was really useful actually! :-)   ...
written 16 months ago by sergio.espeso-gil0
2
votes
2
answers
432
views
2
answers
Extracting non-interacting hic reads to create a sam/bam file
... Hi! I would like to extract the not chimeric reads from hic data and create a bam file with it. I have been trying, but with not much success. I saw that maybe with DiffHic could be feasible (currently checking) or with HiCPro that generates a sam file with the chimeric reads (I need to know how to ...
diffhic hic hicpro written 16 months ago by sergio.espeso-gil0
0
votes
1
answers
397
views
1
answers
Comment: C: Subsampling bam file - error DiffBind
... Thanks!!! That´s was the error, now working fine! I could not live without youuuuuuuu and Rory hahaha  THANKS!!!    ...
written 20 months ago by sergio.espeso-gil0
1
vote
1
answer
397
views
1
answer
Subsampling bam file - error DiffBind
... Hi community! I am subsampling input control data for DiffBind analysis to test something. I have merged first input files by using samtools merge and then later samtools view -s "percentage of subsampling"   When I am trying to run DiffBind, then I get this error: 'subsampled_input.bam'  does n ...
diffbind samtools written 20 months ago by sergio.espeso-gil0 • updated 20 months ago by Gord Brown580
0
votes
1
answers
329
views
1
answers
Comment: C: Providing specific regions to Diffbind
... Thanks Rory   ...
written 23 months ago by sergio.espeso-gil0
1
vote
1
answer
329
views
1
answer
Providing specific regions to Diffbind
... Hi community! I am providing to Diffbind a genomic region list to be analyzed (not peaks, just regions of interest). Although the results are good, I want to avoid Diffbind to merge some of the regions that actually overlap. Can I do that? I have trying so far with no success. Any help?   Thanks! ...
chipseq diffbind written 2.1 years ago by sergio.espeso-gil0 • updated 2.1 years ago by Rory Stark2.6k
0
votes
1
answers
426
views
1
answers
Comment: C: CSAW: getBestTest p-value
... Ok, I see. For whatever reason I though that they could also sort by significance, but in fact they both report a p-value per cluster following different strategies. To sort by significance I need to do section 7.2, rigth?  ...
written 3.2 years ago by sergio.espeso-gil0
2
votes
1
answer
426
views
1
answer
CSAW: getBestTest p-value
... Hi Aaron,  Sorry for being so annoying asking questions, at the end I have decided that predefined regions is not worth it by now (at least), maybe at the future. I have arrived to a good filtering normalisation options for my ChIPs (I think), and I am just merging and getting the windows with stro ...
csaw written 3.2 years ago by sergio.espeso-gil0 • updated 3.2 years ago by Gordon Smyth35k
0
votes
3
answers
573
views
3
answers
Comment: C: CSAW: Annotation through clustering with external information
... Ok, thanks Aaron. I will try. What I also need to ask you is how to enter my own predefined regions, I guess I need to read GRanges documentation, right?  Have a nice day ...
written 3.3 years ago by sergio.espeso-gil0
0
votes
3
answers
573
views
3
answers
Answer: A: CSAW: Annotation through clustering with external information
... Hi Aaron for the answers. Concerning my second question: tabpromoter is setted as follows: olap<- findOverlaps(promoter, rowRanges(filtered)) olap tabpromoter<- combineOverlaps(olap, results.promoter$table) head(tabpromoter[!is.na(tabpromoter$PValue),]) Concerning the error: > test_up ...
written 3.3 years ago by sergio.espeso-gil0 • updated 3.3 years ago by Gordon Smyth35k

Latest awards to sergio.espeso-gil

Popular Question 19 months ago, created a question with more than 1,000 views. For Problem loading bamfiles to ChIPQC
Popular Question 19 months ago, created a question with more than 1,000 views. For edgeR: annotation and isoform analysis alternatives
Popular Question 19 months ago, created a question with more than 1,000 views. For TMM normalisation method
Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 224 users visited in the last hour