User: Jackie
Jackie • 40
- Reputation:
- 40
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- New User
- Location:
- United States
- Last seen:
- 5 days, 1 hour ago
- Joined:
- 5 years, 2 months ago
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Posts by Jackie
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... Thank you, Alex, that's a great resource, and I have downloaded the repeat masker (RM) file, I think combining the list generated using Pierre's code with this file will give a good starting list.
However, I am still trying to understand why, even this RM file is missing some simple repeats, e.g., ...
written 8 days ago by
Jackie • 40
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... Thank you so much for posting the C program. It seems to work perfect, but I have another question. Does this program find only mono- repeats or any repeats with total len >5bp?
...
written 8 days ago by
Jackie • 40
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5 follow
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... I am trying to get a comprehensive list of simple repeats (mono-, di-, tri-, tetra-) in the human genome (hg19). I have downloaded the [simpleRepeat.txt.gz][1] from UCSC, but seems it is missing some of the repeats we are interested in. For example, chr1:981861-981868[CCCCCCCC], chr1:1116223-111623 ...
written 9 days ago by
Jackie • 40
• updated
8 days ago by
Alex Reynolds ♦ 20k
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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 4 months 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 4 months ago by
Jackie • 40
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Comment:
A: GT tag in VCF spec
... Thank you very much. This is helpful! ...
written 5 months ago by
Jackie • 40
4
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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 5 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 6 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 6 months ago by
Jackie • 40
• updated
6 months ago by
shenwei356 • 3.2k
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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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For tophat-fusion for gene fusion detection
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For tophat-fusion for gene fusion detection
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