User: fabbri.marco

gravatar for fabbri.marco
Reputation:
0
Status:
New User
Last seen:
8 hours ago
Joined:
2 years, 7 months ago
Email:
f***********@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 fabbri.marco

<prev • 18 results • page 1 of 2 • next >
0
votes
0
answers
113
views
0
answers
Comment: C: Missing mappability file for mm10
... Thank you but I do not think I can use it for HMMcopy Marco ...
written 6 weeks ago by fabbri.marco0
0
votes
0
answers
113
views
0
answers
Missing mappability file for mm10
... I would like to use HMMcopy and ichorCNA for mm10. It looks there are no Mappability or Uniqueness of Reference Genome from ENCODE for mm10, so I can not generate the segmentation file. Anyone has already produced Mappability files for mm10 and wants to share? Any other suggestions? Thanks Marco ...
mm10 mappability written 6 weeks ago by fabbri.marco0
0
votes
0
answers
156
views
0
answers
Comment: A: Complete exon coordinate for ref seq gene
... In this RefSeq genome annotation file, for example for IL9R we have different exons in different transcripts, some are shared and some unique. I would like to have a single line per gene with the union of exon coordinates: results: IL9R chrX 155997580,156002905,156003448,156003676,15600441 ...
written 3 months ago by fabbri.marco0 • updated 3 months ago by genomax70k
0
votes
0
answers
156
views
0
answers
Complete exon coordinate for ref seq gene
... I have a list of ref-seq genes and I would like to get genome coordinates of all non-overlapping and non-replicated exons for each gene. I am designing a gene panel to detect mutations and I want to be sure to have all exons covered. Any suggestion, how to proceed? thank you Marco ...
exon ref-seq written 3 months ago by fabbri.marco0
0
votes
0
answers
139
views
0
answers
Canonical transcript exon bounderieis
... I have a list of HUGO symbols and would like to get the exon boundaries only of the canonical transcripts. thank you for suggestion ...
canonical exon written 5 months ago by fabbri.marco0
0
votes
1
answer
379
views
1
answer
varscan not taking opstions
... I am running varscan 2.4.3, mpileup2snp is not taking the settings as you can below, it works but with default settings any suggestion how to change them? varscan mpileup2snp sam1 –-min-coverage 10 –-min-var-freq 0.05 –-p-value 0.05 --output-vcf 1 > test6var005.vcf Only SNPs will be rep ...
mpileup2snp varscan2 setting written 15 months ago by fabbri.marco0 • updated 15 months ago by Pierre Lindenbaum122k
0
votes
0
answers
534
views
0
answers
varscan somatic without normal
... I am interested in somatic mutations using a gene panel ( focused on lymphoma). For a sample I do not have the normal counterpart. I would like to use varscan, any suggestion how to run the analysis? Thank you marco ...
varscan mutation written 16 months ago by fabbri.marco0
4
votes
3
answers
2.3k
views
3
answers
Realignment disappeared in gatk4
... In GATK4 the indel realignment step will no longer be part of the pipeline. With my great surprise the tool has disappeared. My question, the algorithm is no more there because it doesn't improve the alignment? Do I need to search for a replace or should I just remove it from my pipeline since it is ...
gatk realignment written 17 months ago by fabbri.marco0 • updated 17 months ago by igor8.1k
0
votes
1
answer
531
views
1
answers
Comment: C: varscan2 somatic sip
... Yes the sounds reasonable, I have to check the settings in varscan. Probably I have to allow to define Germaine above a percentage or number of reads. Any suggestions? ...
written 18 months ago by fabbri.marco0
0
votes
1
answer
531
views
1
answers
Comment: A: varscan2 somatic sip
... I think that I will change my setting, since this is in my opinion is a somatic mutation, there only 2 reads in the normal sample (lymphoma). I check how to set varscan option in a way that this should be predicted as somatic. What do you think? Marco ...
written 18 months ago by fabbri.marco0

Latest awards to fabbri.marco

Popular Question 12 months ago, created a question with more than 1,000 views. For Realignment disappeared in gatk4

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1118 users visited in the last hour