User: noeD

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noeD70
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Posts by noeD

<prev • 47 results • page 1 of 5 • next >
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TCGAbiolink gene expression: normal/tumor pair
... Hello! I have downloaded data from TCGAbiolinks of gene expression: query <- GDCquery(project = "TCGA-BRCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - C ...
tcgabiolinks normal tumor gene_expression written 11 hours ago by noeD70
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smallRNA alignment and counting multimapping
... Hello! I am analyzing smallRNA data of human genome. I have aligned my read against genome with bowtie2: > bowtie2 --end-to-end --very-sensitive -x hg38 -U input_file -S > output_file_align and I used featurescount in order to obtained the counts. For the counting: I used the gtf file with ...
smallrna alignment featurescount written 5 weeks ago by noeD70 • updated 5 weeks ago by Friederike920
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dbsnp hg 38
... Hello! I am using `GATK -T BaseRecalibrator` in my pipeline for whole exon sequencing, and I would like to indicate the -knownSites option, therefore I need the dnsbp file for the hg38. I found at this link https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v ...
dbsnp gatk hg38 baserecalibrator written 10 weeks ago by noeD70 • updated 10 weeks ago by finswimmer660
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variant Recalibrator, -an option
... Hello! I would like to understand the -an option in Variant Recalibrator of GATK. (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php) For example, If I use the `-an DP` option, what will GATK d ...
gatk variant recalibrator -an written 12 weeks ago by noeD70 • updated 12 weeks ago by Pierre Lindenbaum103k
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locateVariants missing some mutation site
... Hello! I am using Variant Annotation package from Bioconductor to annotate my variant but it missed some variants in the output. For example, in `var` I have the following mutation site : CHROM POS REF ALT 9751 chr6 41184897 G A I used `GRanges` for the genomic locati ...
R bioconductor variant annotation written 3 months ago by noeD70
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Comment: C: Cosmic Database using BioMart
... Thank you for your reply. But is it possible to download the database for INDEL mutations? Thank you in advance ...
written 3 months ago by noeD70
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Cosmic Database using BioMart
... Hello! I have read that with BioMart package in R it is possible to download the cosmic database. Unfortunately I didn't understand how to do it. If I use listMart() I see only ensemble-database.. I have tried with listMart(host=http://cancer.sanger.ac.uk/cosmic), but it didn't work... Thank you i ...
R biomart cosmic written 3 months ago by noeD70 • updated 3 months ago by Emily_Ensembl14k
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Comment: C: featuresCount -s 2 option
... I apologize for my stupid question.. but if I have paired-end reads, it doesn't mean that the library is directional? Thank you in advance ...
written 5 months ago by noeD70
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Comment: C: featuresCount -s 2 option
... Thank you for your reply. How can I confirm it? Furthermore, is it normal to obtain that percentage of assigned reads? Thank you in advance for your help! ...
written 5 months ago by noeD70
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featuresCount -s 2 option
... Hello! :) I have paired-end RNA-seq data aligned by STAR, I used featuresCount in order to get read summarization.(I know that STAR can give the count, but I would like to try with featuresCount). I don't understand why if I use the "-s 2" option I obtained a lower number of assigned read than with ...
featurescount rna-seq written 5 months ago by noeD70 • updated 5 months ago by Devon Ryan74k

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