User: Jackie
Jackie • 40
- Reputation:
- 40
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- New User
- Location:
- United States
- Last seen:
- 2 weeks, 5 days ago
- Joined:
- 5 years ago
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- d*******@gmail.com
about me
Posts by Jackie
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... 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! ...
written 9 weeks ago by
Jackie • 40
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... 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 ...
written 9 weeks ago by
Jackie • 40
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Comment:
A: GT tag in VCF spec
... Thank you very much. This is helpful! ...
written 3 months ago by
Jackie • 40
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... 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 ...
written 3 months ago by
Jackie • 40
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... 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 ...
written 4 months ago by
Jackie • 40
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... 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 ...
written 4 months ago by
Jackie • 40
• updated
4 months ago by
shenwei356 • 3.1k
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... 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 ...
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... 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 ...
written 4 months ago by
Jackie • 40
• updated
4 months ago by
Brian Bushnell ♦ 12k
3
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1
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241
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5 follow
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... 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 ...
written 5 months ago by
Jackie • 40
• updated
3 months ago by
Chris Saunders • 100
1
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... 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 ...
written 5 months ago by
Jackie • 40
• updated
3 months ago by
Chris Saunders • 100
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Popular Question
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For tophat-fusion for gene fusion detection
Popular Question
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created a question with more than 1,000 views.
For tophat-fusion for gene fusion detection
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