User: s1469060

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s146906010
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Posts by s1469060

<prev • 14 results • page 1 of 2 • next >
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Comment: C: S4Vectors install error
... Have done, thanks for the tip! All the best, Zoe ...
written 10 months ago by s146906010
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S4Vectors install error
... Hi all I am trying to install packages into my Rstudio. Running R version: 3.4.4. However the packages seem to download fine but then won't load for a lot of them? So for S4Vectors the download proceeded as follows: > biocLite("S4Vectors") BioC_mirror: https://bioconductor.org Usi ...
R rna-seq written 10 months ago by s146906010
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Comment: C: XVector install error
... Actually, it may be a problem with the isnullptr package which appears to be correctly installed, and is in my library. However when I try to load gives the error: library(isnullptr) Error: package or namespace load failed for ‘isnullptr’ in FUN(X[[i]], ...): no such symbol isnullptr_ ...
written 10 months ago by s146906010
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(Closed) XVector install error
... Hi all I'm trying to load the XVector package into R studio. I installed the package via R (which is correctly synced to Rstudio) and is successful- version 3.6 of R and version 3.9 of XVector. However whilst the library appears on my list I won't load properly. Error as follows: library(XVe ...
R written 10 months ago by s146906010
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Comment: C: Picard MarkDuplicates flag vs remove issue
... Sorry if that wasn't clear enough. Original read file: 59 million reads. The commands are as follows: java -jar /exports/igmm/eddie/hill-lab/Zoe/References_and_Scripts/picard-tools-2.5.0/picard.jar MarkDuplicates I=Mutant1_paired_align_subMitoUnc_sorted.bam O=Mutant1_align_filtered.bam M=Mutant1_te ...
written 22 months ago by s146906010
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Comment: C: Picard MarkDuplicates flag vs remove issue
... Hi, thanks for the reply. But I'm still a bit confused. It's not that using Samtools rmdup is removing fewer reads, I have never even tried it. It's just that when I remove the reads flagged as duplicates by MarkDuplicates rather than using its own REMOVE_DUPLICATES=TRUE option I am getting differen ...
written 22 months ago by s146906010
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Picard MarkDuplicates flag vs remove issue
... Hi all I have "a quick question" about Picard MarkDuplicates. I have ATAC-seq data, already filtered for mitochondrial and unmapped reads. The initial file has about 59 million reads. When I run MarkDuplicates as so: java -jar /exports/igmm/eddie/hill-lab/Zoe/References_and_Scripts/picard-tools- ...
duplicates picard atac-seq markduplicates written 22 months ago by s146906010 • updated 22 months ago by Prakash1.8k
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Comment: C: Stupid edgeR question
... data_raw <- read.delim("/Volumes/igmm/hill-lab/Zoe/RNA-seq/E12.5_G2-67/DEseq/merged_counts.txt", header=T) rownames(data_raw) <- data_raw$gene data_raw <- data_raw[,-1] data_rawGroups <- c("WT", "WT", "Mutant", "Mutant") mobAnnotation <- read.delim("/Volumes/igmm/h ...
written 2.8 years ago by s146906010 • updated 2.8 years ago by WouterDeCoster43k
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Comment: C: Stupid edgeR question
... Hi Sorry for the delayed reply. This is the full command line: data_raw <- read.delim("/Volumes/igmm/hill-lab/Zoe/RNA-seq/E12.5_G2-67/DEseq/merged_counts.txt", header=T) rownames(data_raw) <- data_raw$gene data_raw <- data_raw[,-1] data_rawGroups <- c("WT", "WT", "Muta ...
written 2.8 years ago by s146906010 • updated 2.8 years ago by WouterDeCoster43k
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Answer: A: HT-seq count memory error
... Just to post the solution to this. I'm not sure why it was a problem seeming as HTseq should work with order specified as pos or name and with sam or bam input, but it seemed to work fine when I changed to bam input format and sorted by name. Not sure why this mattered but it worked! Thanks. Zoe ...
written 2.9 years ago by s146906010

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Popular Question 22 months ago, created a question with more than 1,000 views. For HT-seq count memory error

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