User: noeD

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noeD70
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Posts by noeD

<prev • 51 results • page 1 of 6 • next >
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proteins.actions file of string
... Hello! I have downloaded proteins.actions file for homo sapiens from STRING db. The column names of the files are: > item_id_a item_id_b mode action is_directional > a_is_acting score here I have found the meaning: https://blog.csdn.net/mystrugglelife/article/de ...
network string written 7 weeks ago by noeD70
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Filtering lowly expressed genes - edgeR
... Hello! I have read on EdgeR guideline, section 4.1.4 "RNA-Seq of oral carcinomas vs matched normal tissue" (http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf) this suggestion for filtering lowly expressed genes: > Normally we would also filter low ...
R filtering rna-seq edger written 5 months ago by noeD70 • updated 5 months ago by Santosh Anand3.5k
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Comment: C: rna-seq analysis of tumor/normal pairs
... thank you... How can I set the threshold for minimum counts for gene? ...
written 5 months ago by noeD70
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Comment: C: rna-seq analysis of tumor/normal pairs
... thank you... How can I set the threshold for minimum counts for gene? ...
written 5 months ago by noeD70
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Comment: C: rna-seq analysis of tumor/normal pairs
... thank you but I have only the counts. ...
written 5 months 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 6 months ago by noeD70 • updated 6 months ago by Friederike1.8k
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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 7 months ago by noeD70 • updated 7 months ago by finswimmer2.9k
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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 8 months ago by noeD70 • updated 8 months ago by Pierre Lindenbaum108k
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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 8 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 8 months ago by noeD70

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