User: cilgaiscan

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cilgaiscan30
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Turkey
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cilgaiscan
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2 months, 4 weeks ago
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Posts by cilgaiscan

<prev • 21 results • page 1 of 3 • next >
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Comment: C: How to change colour of points in volcano plot by common genes?
... i will look for this link. and i am already using the col argument in my code but the problem the things i would like to color is in different dataframe.. ...
written 3 months ago by cilgaiscan30
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How to change colour of points in volcano plot by common genes?
... this is my code to draw volcano plot. but i need to give green dots color for genes in up; red ones for genes in down. how can i do? down<- intersect(down_our$hgnc_symbol,down_pre$Gene) up<-intersect(up_our$hgnc_symbol,up_pre$Gene) res <- read.table(file = "path for csv", ...
deseq2 log2fc volcano plot rna-seq written 3 months ago by cilgaiscan30 • updated 3 months ago by Kevin Blighe33k
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Answer: A: Get gene names from ensembl ID or gene region
... Hey! I use biomaRt in R. Here is my code for it. Hope it will help : library("biomaRt") differentialexpression <- read.csv("put your file's path here", sep = ",",header = T) ensembl = useMart("ensembl", dataset="mmusculus_gene_ensembl") values<- differentialexpression$colum ...
written 3 months ago by cilgaiscan30
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Comment: C: Difference between two count table that created from same fastq files?
... Yes it is listed as supplementary file down the website. I am sending the link where you can download and see [Count table][1] [1]: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64529/suppl/GSE64529%5FCountsTable%2Etxt%2Egz ...
written 3 months ago by cilgaiscan30
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Comment: C: Difference between two count table that created from same fastq files?
... I am using bam files which are outputs of tophat2 with paired-end reads. To check that I am okay with alignment, I have bam files gathered by STAR aligner with exact fastq files. And in both alignments my alignment score is around 91-94%. And I gathered fastq files with corresponding SRR numbers w ...
written 3 months ago by cilgaiscan30
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Comment: C: Difference between two count table that created from same fastq files?
... I suppose, they are using NCBI Refseq UCSC for hg19. Because counts appear as NM_013943 instead of NM_013943.2 So, that leaves being ENSEMBL or GENCODE out I assume. Also it leaves to be NCBI curated, aligned or all, too. Assuming that they are using NCBI Refseq UCSC, I am using it where I gt from [ ...
written 3 months ago by cilgaiscan30
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Comment: C: Difference between two count table that created from same fastq files?
... 1. I suppose, they are using NCBI Refseq UCSC ann. hg19 as well as I am using it too. Because counts appear as NM_013943 instead of NM_013943.2 So, that leaves being ENSEMBL or GENCODE I assume. Also it leaves to be NCBI curated, aligned or all, too. Assuming that they are using NCBI Refseq UCSC, I ...
written 3 months ago by cilgaiscan30
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Comment: C: Difference between two count table that created from same fastq files?
... actually I runned featurecounts with -p option, too. but results come same. again i have 66k counts.and i checked for dublicates or different naming of same gene but all came negative. they are unique 66k counts. ...
written 3 months ago by cilgaiscan30
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Comment: C: Difference between two count table that created from same fastq files?
... I have pair-end and did pair-end alignment with tophat2 And featureCounts recognizes my bams from paired end data as expected. I used tophat2 (v.2.1.0), and featureCounts (v.1.5.0) with hg19 (Febr. 2009, NCBI RefSeq). I used default options.. for tophat2: tophat2 hg19 (with a full path wh ...
written 3 months ago by cilgaiscan30 • updated 3 months ago by RamRS19k
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Comment: C: Difference between two count table that created from same fastq files?
... both of our count tables are created by NCBI refseq gtf files. I am sure that I use NCBI Refseq but theirs appears so. but there's 28k difference which is very huge. I checked for XM's and XR'S both count table does not contain any of those. And firstly, I thought there might be a problem in my a ...
written 3 months ago by cilgaiscan30

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