https://bioinfo.cipf.es/projects/ 2026-04-24T10:27:48+0200 https://bioinfo.cipf.es/projects/ https://bioinfo.cipf.es/projects/lib/tpl/arctic/images/favicon.ico text/html 2015-07-13T12:36:15+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:b24_coverage?rev=1436783775&do=diff A. Relationship between size region and its coverage text/html 2015-07-13T13:21:12+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:b25_coverage?rev=1436786472&do=diff B. Are there coverage differences by run? When comparing averages of total counts between 4 runs, the second one shows the lowest average (254 524 616) but these differences aren't significant relative to the rest of groups (Kruskal-Wallis test: chi-squared = 4.3443, df = 3, p-value = 0.2266). So, the coverage is consistent along different runs. text/html 2015-07-07T10:09:25+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:bier_methods?rev=1436256565&do=diff Bioinformatics Analysis A. Sequencing Processing Raw reads were generated from the standard Illumina pipeline with default options. We performed a quality control of fastq files using FastQC (1). B. Mapping We used the mouse sequenced genome: GRCm38. The fasta file containing sequences of this genome was downloaded from Ensembl ( text/html 2015-07-07T16:56:39+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:bier_results?rev=1436280999&do=diff Results A. Sequence processing This table shows number of giga base pairs and descriptive indicators by run. * run: this experiment included 4 runs * total_Gb: total Gb (giga base pairs = 1000000000 bp) by run * total_bb: total bp (base pairs) by run text/html 2015-07-07T09:36:18+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:dnanexus_coverage?rev=1436254578&do=diff text/html 2015-07-12T16:24:23+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:dnanexus_mapping?rev=1436711063&do=diff A.2.2. Mapping This table shows number of mapped reads and quality evaluation for each sample: run* sampleID mapped_reads quality report 1 DNA_121 2857379 1 DNA_554 3640785 1 DNA_571 3243827 1 DNA_708 2535679 1 DNA_837 3273816 1 DNA_872 text/html 2015-07-07T10:12:32+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:dnanexus_methods?rev=1436256752&do=diff Bioinformatics analysis Raw reads were generated from the standard Illumina pipeline with default options. The original mappings are just the reads mapped to the genome via BWA mem. The refined mappings are the original mappings which have been put through the text/html 2015-07-09T19:23:43+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:dnanexus_results?rev=1436462623&do=diff Results A. Sequence processing This table shows number of giga base pairs and descriptive indicators by run. * run: this experiment included 4 runs * total_Gb: total Gb (giga base pairs = 1000000000 bp) by run * total_bb: total bp (base pairs) by run text/html 2015-07-10T16:08:28+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:dnanexus_sequencing?rev=1436537308&do=diff A.2.1. Sequence processing A.2.1.1. Description by run This table shows number of giga base pairs and descriptive indicators by run. * run: this experiment included 4 runs * total_Gb: total Gb (giga base pairs = 1000000000 bp) by run * total_bb text/html 2015-07-12T15:41:18+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:dnanexus_variant?rev=1436708478&do=diff A.2.3. Variant calling For each VCF file, several statistical indicators about variant calling were calculated from VARIANT: * run: 4 runs were performed for this study. Run 1 included all 11 controls: patients with known mutations. * sampleID: ID for each sample. text/html 2015-07-13T13:24:29+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:kit_cap_description?rev=1436786669&do=diff Description of capture kit Capture kit includes 56 genes, 862 regions, 465465 bases. text/html 2015-07-07T08:52:53+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:kit_description?rev=1436251973&do=diff Description of capture kit Capture kit includes 57 genes, 847 targets, 465465 bases. Detailed description by genes and targets: A. Description by genes B. Description by targets Information for each target: * target: chromosomal region * gene text/html 2015-07-07T09:37:27+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:kitcap_description?rev=1436254647&do=diff Description of capture kit Capture kit includes 57 genes, 847 targets, 465465 bases. Detailed description by genes and targets: A. Description by genes B. Description by targets Information for each target: * target: chromosomal region * gene text/html 2015-07-07T14:11:35+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:mapping_more?rev=1436271095&do=diff Mapping differences between two pipeline analysis run sampleID mapped_reads_BIER mapped_reads_DNAnexus difference 1 DNA_121 2971616 2857379 114237 1 DNA_554 3999706 3640785 358921 1 DNA_571 3586080 3243827 342253 1 DNA_708 2826124 2535679 290445 1 text/html 2015-07-09T17:29:38+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:prueba?rev=1436455778&do=diff prueba targetgenenbasesexonsCellBaseGenomeMaps1:6527381-6528802PLEKHG51421yeslinklink1:6528861-6529969PLEKHG51108yeslinklink1:6530230-6532104PLEKHG51874yeslinklink1:6532387-6532843PLEKHG5456yeslinklink1:6532913-6533803PLEKHG5890yeslinklink1:6533827-6534847PLEKHG51020yeslinklink1:6534858-6536208PLEKHG5 text/html 2015-07-27T15:46:14+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:start?rev=1438004774&do=diff Assessment of targeted next generation sequencing as a tool for the diagnosis of Charcot-Marie-Tooth disease and hereditary motor neuropathy Charcot-Marie-Tooth disease (CMT) is characterized by broad genetic heterogeneity with more than 50 known disease-associated genes. Mutations in some of these genes can cause a pure motor form of hereditary motor neuropathy (HMN), the genetics of which are poorly characterized. We have designed a panel comprising 56 genes associated with CMT/HMN. We val… text/html 2015-07-10T13:36:16+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:statistics_for_target_and_run?rev=1436528176&do=diff Statistics for target and run Target gene nbases mean_allsamples median_allsamples minimum_allsamples mean_run1median_run1 minimum_run1 mean_run2 median_run2 minimum_run2 mean_run3 median_run3 minimum_run3 mean_run4 median_run4 minimum_run4 1:6527380-6528802 text/html 2015-07-10T14:51:14+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/projects/espinos:stats_target?rev=1436532674&do=diff Statistics for target and run target gene nbases mean_all med_all min_all mean_r1med_r1 min_r1 mean_r2 med_r2 min_r2 mean_r3 med_r3 min_r3 mean_r4 med_r4 min_r4 1:6527380-6528802 PLEKHG5 1422 800.6 795.1 572.7 788.5 795.1 709.0 771.8 776.6 715.3 782.5