User: jls2282

gravatar for jls2282
jls22820
Reputation:
0
Status:
New User
Last seen:
2 years, 10 months ago
Joined:
4 years, 10 months ago
Email:
j******@columbia.edu

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

This helps us discourage the inappropriate use of our site.

Posts by jls2282

<prev • 6 results • page 1 of 1 • next >
0
votes
1
answer
459
views
1
answer
TarSeqQC TargetExperiment() example takes forever
... When running TarSeqQC the system hangs with only one rsession thread at 100% for at least 20 minutes (Mac Pro 2 x 3.06 GHz 6-core Intel Xeon processors, 128 GB 1333 MHz DDR3). I stopped it then since this is too long for a simple example, would not work for an amplicon sequencing analysis pipeline. ...
tarseqqc written 2.8 years ago by jls22820 • updated 2.3 years ago by bioinf10
0
votes
0
answers
538
views
0
answers
Comment: C: gmapR failure to build TP53Genome in osx
... That did it, thanks! ...
written 2.8 years ago by jls22820
0
votes
0
answers
538
views
0
answers
Comment: C: gmapR failure to build TP53Genome in osx
... Thanks for the info. In fact the same R library (shared on Dropbox) is used by two different machines. But I tried to uninstall gmapR and reinstall it on the same machine and did not fix the problem. ...
written 2.8 years ago by jls22820
1
vote
0
answers
538
views
0
answers
gmapR failure to build TP53Genome in osx
... Unable to follow examples with gmapR failing at the stage of gmapR::TP53Which()     .libPaths('~/Dropbox/R_packages/library/') library(gmapR) gmapR::TP53Genome() Fails with following message: 'select()' returned 1:1 mapping between keys and columns -b flag not specified, so building with defa ...
gmapr written 2.9 years ago by jls22820
0
votes
1
answer
946
views
1
answers
Answer: A: readVCF (VariantAnnotation) problem with mismatched header and info fields in vc
... OK, maybe not the most elegant solution, but here is code that fixes the vcf header on a vcfF file:   #Find 1st header block library(data.table) row=1 while(substr(fread(vcfF,nrows = 1,skip=row-1,header = F,sep="\n"),1,6)!="##INFO"){   row=row+1 } first row<-row header1<-fread(vcfF,nrows=fi ...
written 4.9 years ago by jls22820
0
votes
1
answer
946
views
1
answer
readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
...   I am having a problem reading the info field on vcf files generated by the NextGene software. Here is an example: vcfF is the vcf report as exported from NextGene >hdr=scanVcfHeader(vcfF) > rownames(info(hdr)) [1] "NS" "DP" ...
variantannotation annotation vcf readvcf written 4.9 years ago by jls22820

Latest awards to jls2282

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 122 users visited in the last hour