User: beanavarro85

gravatar for beanavarro85
Reputation:
0
Status:
New User
Last seen:
2 days, 9 hours ago
Joined:
5 years, 6 months ago
Email:
b***********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by beanavarro85

<prev • 8 results • page 1 of 1 • next >
0
votes
2
answers
123
views
2
answers
Comment: C: Soft filtering of SNPs in a list
... I believe [VariantFiltration][1] adds "filter_name", but I am unsure on how provide a SNP list as a filter expression. I have never used [PyVCF][2], I'll check that out. [1]: https://gatk.broadinstitute.org/hc/en-us/articles/360037434691-VariantFiltration [2]: https://pyvcf.readthedocs.io/en ...
written 6 weeks ago by beanavarro850
0
votes
2
answers
123
views
2
answers
Soft filtering of SNPs in a list
... Hi all! I am looking for a way to filter a list of SNPs from a VCF file. I know that, with GATK SelectVariants or VCFtools you can exclude a list of SNPs from your VCF, however what I want is to soft-filter them (add filter info in the FILTER column of the VCF). Any ideas? Thanks! ...
snp written 6 weeks ago by beanavarro850 • updated 6 weeks ago by finswimmer13k
0
votes
3
answers
8.5k
views
3
answers
Comment: C: LD-decay in a r2 vs distance(cm) plot
... This post is great! I am getting into the same issue, did you find a solution? Would you mind to share? Thanks, Beatriz ...
written 14 months ago by beanavarro850
0
votes
2
answers
1.2k
views
2
answers
Comment: C: Stats on the overlapping length within two bed files
... I was sure there was a way to do it in one line, but didn't know how! ...
written 2.2 years ago by beanavarro850
0
votes
2
answers
1.2k
views
2
answers
Comment: C: Stats on the overlapping length within two bed files
... Awesome! Thanks, it worked perfectly. Since the order won't change, I have pasted this two columns to my reference.bed file like this: $ bedmap --echo-overlap-size reference.bed map.bed | awk '{ s=0; t=0; n=split($0, a, ";"); for(i = 1; i <= n; i++) { if(a[i] > 100) { s += a[i]; t++; } ...
written 2.2 years ago by beanavarro850
0
votes
2
answers
1.2k
views
2
answers
Comment: C: Stats on the overlapping length within two bed files
... Thanks! I will next time, sorry about that. ...
written 2.2 years ago by beanavarro850
1
vote
2
answers
1.2k
views
2
answers
Stats on the overlapping length within two bed files
... Hi all, I have two bed files, and I have run bedtools intersect to calculate the overlapping regions. bedtools intersect -a fileA.bed -b fileB.bed -wao > overlaps.bed I need to calculate the number of overlaps that are longer than 100 bp (i.e. value higher than 100 in the 8th column of ...
bedtools genome bedops written 2.2 years ago by beanavarro850 • updated 2.2 years ago by Alex Reynolds30k
0
votes
1
answer
2.2k
views
1
answers
Answer: A: How to do goseq with user created "lenghtData" and category mapping objects?
... Hi! I have the same problem here, did you get any answers or find a solution? Thanks! ...
written 5.5 years ago by beanavarro850

Latest awards to beanavarro85

Popular Question 10 months ago, created a question with more than 1,000 views. For Stats on the overlapping length within two bed files

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 839 users visited in the last hour