User: lamia_203

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lamia_20330
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Posts by lamia_203

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How to combine count matrix with mouse gene information from Ensemble using Biomart in R
... Hi, I am trying to add a row of gene id next to my rows of gene symbols. normlaised_mouse3 is my count matrix for rna-seq analysis. I've used to code: library('biomaRt') normalised_mouse_biomart <- read.delim("normalised_mouse3.txt") mart <- useDataset("mmusculus_gene_ensembl", u ...
ensembl biomart rna-seq R written 6 months ago by lamia_20330 • updated 6 months ago by zx87548.2k
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Comment: C: Aligning using hg18
... The genome was used before and aligned fine and gave reads at expected genes for another study I carried out (beta cells), however I am also unsure as to why it didn't map the reads I provided (they are human as well). The parameters were kept the same as before as well: for i in *.fq.gz; do ST ...
written 7 months ago by lamia_20330
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Comment: C: Aligning using hg18
... Thank you. I downloaded it from [UCSC][1] I believe, I couldn't find the gtf files clearly on there. This is my first time downloading genomes hence why I am unclear. [1]: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ ...
written 7 months ago by lamia_20330 • updated 7 months ago by RamRS24k
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Comment: C: Aligning using hg18
... Many thanks! Yes, I tried aligning it to recent genome GRCh38 but the counts all appeared as 0 for genes and were all unmapped after QC. So I am trying to align the samples to the genome that the study have used. I am not sure why there were unmapped reads for GRCh38 as I had used it to previously a ...
written 7 months ago by lamia_20330
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Aligning using hg18
... Hi, I'm trying to align reads from a study but they have aligned it to hg18. I managed to get the hg18.fa file in and want to align the samples to it. The code I am using is: for i in *.fq.gz; do STAR --./hg18.fa --runMode alignReads --readFilesIn $i --readFilesCommand ...
annotation alignment hg18 rna-seq written 7 months ago by lamia_20330 • updated 7 months ago by h.mon27k
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Na values when normalising using SCnorm
... Im trying to run normalization using SCnorm in R. The normalization is running fine on the first dataset but the second dataset is coming up with an error message: Error in if (any(colSums(SingleCellExperiment::counts(Data)) == 0)) { : missing value where TRUE/FALSE needed When checking ...
R missing values na rna-seq scnorm written 7 months ago by lamia_20330
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Comment: C: Creating Count Matrix
... This does use all the sample thank you. How does the loop for the i part work? When I ran this code, the count_matrix included two repeated columns from each sample rather than one. Thanks ...
written 7 months ago by lamia_20330
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Comment: C: Creating Count Matrix
... Sorry I didn't specify. I'm familiar with R and Linux but prefer to make the count table in Linux since there are a lot of samples (about 3200). ...
written 7 months ago by lamia_20330
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Creating Count Matrix
... I have to create a count table with: Gene ID Sample1 Sample2 Sample3 ENSG... 297 0 0 So far I have files with their individual tables, it contains 4 columns with Gene ID, and the remaining three columns read counts. I want to take the second column from each sample and ma ...
rna-seq linux written 7 months ago by lamia_20330 • updated 7 months ago by ahaswer150
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How to speed up trimming using trim galorer
... I am currently trying to follow a scRNA-seq pipeline, however I have encountered a couple of problems.When trying to trim a paired-end read sample to remove reads with a quality score below 20 using trim galore, for one particular sample it is has been running for over 12 hours and has only done 4 o ...
fastq rna-seq trim written 8 months ago by lamia_20330 • updated 8 months ago by mbk0asis460

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