User: Jackie

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Jackie40
Reputation:
40
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New User
Location:
United States
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5 days, 1 hour ago
Joined:
5 years, 2 months ago
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Posts by Jackie

<prev • 31 results • page 1 of 4 • next >
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Comment: C: How to extract all the simple repeats from the hg19 reference genome
... 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 Jackie40
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Comment: C: How to extract all the simple repeats from the hg19 reference genome
... 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 Jackie40
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How to extract all the simple repeats from the hg19 reference genome
... 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 ...
simple repeats reference genome written 9 days ago by Jackie40 • updated 8 days ago by Alex Reynolds20k
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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 months ago by Jackie40
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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 4 months ago by Jackie40
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Comment: A: GT tag in VCF spec
... Thank you very much. This is helpful! ...
written 5 months ago by Jackie40
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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 5 months ago by Jackie40
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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 6 months ago by Jackie40
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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 6 months ago by Jackie40 • updated 6 months ago by shenwei3563.2k
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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 6 months ago by Jackie40 • updated 6 months ago by genomax32k

Latest awards to Jackie

Popular Question 3 months ago, created a question with more than 1,000 views. For tophat-fusion for gene fusion detection
Popular Question 7 months ago, created a question with more than 1,000 views. For tophat-fusion for gene fusion detection

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