User: mariafirulevabio

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Posts by mariafirulevabio

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Extract GEO for certain experiment type
... Hi genomax, Thanks for your advice. I suppose I should not only 'scRNAseq' but other terms because after intersection my list (1315 elements) with the got list from I found only 4 common accession numbers. Could you prompt me how I can get direct links to files that correspond to the accession num ...
written 9 weeks ago by mariafirulevabio40
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Extract GEO for certain experiment type
... Dear all, Suppose I have a big list of GEO's corresponding certain experiment type (e.g., sc-RNA-seq). How can I extract all GEO's for target experiment type (sc-RNA-seq, in this case) and, after comparison all available GEO with my list, extract direct links for files which are presented in selec ...
geo gsm geo accession bioconductor written 9 weeks ago by mariafirulevabio40
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Unindexed clusters: Illumina
... Dear all, Could you please explain the concept of "Unindexed clusters" as a result of Illumina sequencing? What leads to the appearance of such clusters? How do I interpret a high or low percentage of such clusters in my results? Also, what "filters" are appealed to clusters that are marked "PF" in ...
ilumina clusters illumina index written 10 weeks ago by mariafirulevabio40 • updated 10 weeks ago by genomax71k
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Answer: A: tumor only variant calling tools
... This [paper][1] provide information about different variant callers, including variant callers with available tumor-only mode. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5852328/ ...
written 11 weeks ago by mariafirulevabio40
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Comment: C: Target cancer sequencing: can't find database with raw data and related publicat
... Thanks, Kevin! I suppose it is better for me to choose a target panel which doesn't overlap complicated regions (repeats, high GC-content sequences, etc). ...
written 12 weeks ago by mariafirulevabio40
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Answer: A: Target cancer sequencing: can't find database with raw data and related publicat
... Since I've not found the answer, I guess these links ([post][1], [paper][2]) will be useful for someone with the same aims. I've decided to use a mixture of two Genome in a Bottle samples (truth set is available) for somatic variant calling validation. There is an option to choose a desired gene pa ...
written 12 weeks ago by mariafirulevabio40
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Imputation of scRNA-seq data
... There are several tools for imputation of scRNA-seq data, most of them have released in 2018-2019. Since these programs were announced recently, it is complicated to find info about user' choice, except several articles for comparison several of these tools (e.g., [this][1]). Will you provide me you ...
scrna-seq imputation rna-seq written 12 weeks ago by mariafirulevabio40
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Comment: C: Target cancer sequencing: can't find database with raw data and related publicat
... Is a biological validation a costly and time-consuming task for variants from targeted sequencing? Can validation be performed only for the pool of interested variants (e.g., hot spots)? Cyriac addressed to NCI's GDC Legacy Archive for validated BAM files, however, it is a bioinformatic validation. ...
written 12 weeks ago by mariafirulevabio40
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Comment: C: Compendium of validated somatic variant calls with associated reads and referenc
... I guess you can find the answer using this [FAQ][1]. [1]: https://gdc.cancer.gov/about-gdc/gdc-faqs ...
written 12 weeks ago by mariafirulevabio40
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Comment: C: Target cancer sequencing: can't find database with raw data and related publicat
... I need annotated VCF files (or BAM with variant calling description, if it was done) as *in silico* control for bioinformatics pipeline and, also, I need wet lab confirmation of observed variant allele frequencies. I guess, my question is similar to this [post][1]. [1]: https://www.biostars.org/ ...
written 12 weeks ago by mariafirulevabio40

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