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 months 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 10 months ago by noeD70 • updated 10 months ago by Santosh Anand4.3k
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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 10 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 10 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 10 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 12 months ago by noeD70 • updated 12 months ago by Friederike2.3k
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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 13 months ago by noeD70 • updated 13 months ago by finswimmer7.8k
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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 13 months ago by noeD70 • updated 13 months ago by Pierre Lindenbaum115k
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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 14 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 14 months ago by noeD70

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Commentator 14 months ago, created a comment with at least 3 up-votes. For C: How can I input a BAM file to the samtools mpileup command without using a text

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