User: Jackie

gravatar for Jackie
Jackie40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
an hour ago
Joined:
4 years, 12 months ago
Email:
d*******@gmail.com

about me

Posts by Jackie

<prev • 28 results • page 1 of 3 • next >
0
votes
0
answers
192
views
0
answers
benchmarking/validation tools for CNVs
... Are there good benchmarking/validation tools for CNVs? By 'benchmarking/validation', I mean, you feed the tool a truth set and the CNVs called by a CNV caller, then the tool will output something like the sensitivity and specificity of the CNV caller. Thanks! ...
truth set benchmarking cnv validation written 4 weeks ago by Jackie40
0
votes
0
answers
89
views
0
answers
CNV tools for hybridization vs. amplicon capture WES data
... In this review paper (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S11-S1), it lists several tools that are suitable for CNV detection with WES data (e.g., Control-FREEC, CoNIFER, XHMM, ExomeCNV, CONTRA), but it does not mention whether these tools work well with the hy ...
amplicon cnv hybridization bioinformatics tools written 5 weeks ago by Jackie40
0
votes
1
answer
133
views
1
answers
Comment: A: GT tag in VCF spec
... Thank you very much. This is helpful! ...
written 9 weeks ago by Jackie40
4
votes
1
answer
133
views
1
answer
GT tag in VCF spec
... Hi, Is GT tag in the FORMAT col a required tag by VCF spec? If a VCF does not have GT tag, is it still a valid VCF? Or put it another way, what is the minimum information that makes a VCF valid? Thanks ...
vcf gt tags valid written 9 weeks ago by Jackie40
0
votes
0
answers
152
views
0
answers
What does 'frac' mean in cufflinks output transcripts.gtf
... In Cufflinks output transcripts.gtf, there is a field called 'frac'. What does that mean? chr1 Cufflinks transcript 18957500 19062632 361 + . gene_id "PAX7"; transcript_id "NM_002584.2"; FPKM "218.4530519923"; frac "0.219171"; conf_lo "200.428676"; conf_h ...
fpkm cufflinkts frac written 3 months ago by Jackie40
0
votes
1
answer
184
views
1
answer
How to output a pdf with both tables and plots using perl
... Hi, I am using perl PDF:Table module to generate a pdf file. In the PDF, there will be 4 sections, 1st, 2nd, and 4th sections are all tables, and the 3rd section needs to be a histogram. Can someone advise how can this be done? I know how to make a PDF with all the sections being tables, but not ...
perl histogram pdf:table plot written 3 months ago by Jackie40 • updated 3 months ago by shenwei3563.0k
0
votes
0
answers
195
views
0
answers
How to map NCBI contig positions to chromosome positions
... I need to make a file which includes all coordinates for human 37.13 (NCBI) ribosomal RNAs. I have downloaded the NCBI 'ref_GRCh37.p13_scaffolds.gff3.gz' file from this link ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ This gff3 file does include the coordinat ...
ncbi contig ribosomal grch37.13 written 3 months ago by Jackie40 • updated 3 months ago by genomax27k
2
votes
1
answer
216
views
1
answer
Use Bowtie to trim reads in fastq files
... I usually use Bowtie as an aligner, but I wonder whether I can use Bowtie as a trimmer as well? I tried the below command line: bowtie -1 read1.fastq -2 read2.fastq --trim5 2 --un unaligned --al aligned > aligned.bam I wanted bowtie to trim the first 2bps at the 5prime end, and outpu ...
trim bowite written 3 months ago by Jackie40 • updated 3 months ago by Brian Bushnell11k
3
votes
1
answer
224
views
5 follow
1
answer
Difference between the two models in manta
... What is the difference between the manta disease model (--tumorBam) and germline model (--bam)? i.e, different calling algorithms, different filtering criteria? Is there some detailed documentation on that? Thanks ...
manta rna-seq written 4 months ago by Jackie40 • updated 9 weeks ago by Chris Saunders100
1
vote
1
answer
225
views
1
answer
Questions about the splitting/spannings reads reported by manta
... Has anyone used the SV caller manta? I have a couple of questions regarding the splitting/spanning reads reported by manta: 1) In the manta output 'diploidSV.vcf', there are PR and SR tags, which mean 'Spanning paired-read support for the ref and alt alleles in the order listed' and 'Split reads fo ...
manta splitting reads spanning reads rna-seq written 4 months ago by Jackie40 • updated 9 weeks ago by Chris Saunders100

Latest awards to Jackie

Popular Question 20 days ago, created a question with more than 1,000 views. For tophat-fusion for gene fusion detection
Popular Question 4 months ago, created a question with more than 1,000 views. For tophat-fusion for gene fusion detection

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1260 users visited in the last hour