User: annaA

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annaA10
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Posts by annaA

<prev • 26 results • page 1 of 3 • next >
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Comment: C: merge samples in phyloseq returns NAs
... yeah but do you see that some of the variables are changed for example the variable "primer" in the new object is translated to numeric values? I am using version 1.32.0 A ...
written 22 days ago by annaA10
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Comment: C: merge samples in phyloseq returns NAs
... In my data there are 3 samples with the same sample name( i.e "sample") FDR0033 lets say.So I thought if I merge them by "sample" it will work.But from what you are saying this is not correct. So I need to add a new variable "x" in which I will give the same name to these 3 samples only(?) and merge ...
written 22 days ago by annaA10
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Comment: C: merge samples in phyloseq returns NAs
... Sure ! next time I'll do it right ...
written 22 days ago by annaA10
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Comment: A: merge samples in phyloseq returns NAs
... Hey thanks for your reply . So the output of the str(sample_data(f_data)) is the following 'data.frame': 237 obs. of 15 variables: Formal class 'sample_data' [package "phyloseq"] with 4 slots ..@ .Data :List of 15 .. ..$ : chr "G1" "G10" "G100" "G101" ... .. ..$ : ...
written 22 days ago by annaA10
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merge samples in phyloseq returns NAs
... Hello I am working in a dataset which contains several categorical variables in the meta data (sample_data). i want to merge some replicates and maybe in the next steps I will need to merge other samples to. To do so I am using the merge_samples function as follows f_data: original phyloseq object ...
R biom phyloseq written 22 days ago by annaA10
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filter OTU table based on absolute abundance
... Hello, Currently I am working with 16S rRNA - metabarcoding data. I have a question about filtering the OTU table prior to downstream analysis. From my reading I am not sure if I should filter the OTU table based on absolute abundance or relative abundance. I know its super basic question, but it ...
metabarcoding microbiome otu written 5 weeks ago by annaA10 • updated 5 weeks ago by antonioggsousa850
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Comment: C: erros in dowloading SRA data
... Thanks for the recommendation I will check it right away! ...
written 6 weeks ago by annaA10
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erros in dowloading SRA data
... Hello, I am downloading a data set from SRA with the following code ; # filename= 'SRR_Acc_List_snRNA.txt' while read line;do echo "Line No. $n : $line" fastq-dump --split-files --gzip $line -O /data/scratch/anna9230/Khrameeva_data /snRNA_data/ ...
sra written 6 weeks ago by annaA10 • updated 6 weeks ago by ATpoint36k
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Comment: C: low mappability of scRNA data
... Hello, Thanks for your reply and the info.Smart2-Seq doesn't have UMIs, that's the only difference I have found some online tutorials in which it's not clear if I need to remove cells with low mappability prior to downstream analysis. But us you said and based on Seurat's tutorials probably I don' ...
written 8 weeks ago by annaA10
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low mappability of scRNA data
... Hey everyone, I am analyzing scRNA data from Smart2-seq . I did the mapping by using Hisat2 .Some of the cells has reaaly low mapping rate (8%) us expected. I am wondering do I need to exclude these cells before the following steps ( filtering with samotools, featureCounts) or they can be excluded ...
scrna-seq mapping rna-seq sequencing written 8 weeks ago by annaA10 • updated 8 weeks ago by ATpoint36k

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