User: patelk26

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patelk26100
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Bioinformatics Scientist I working at The Children's Hospital of Philadelphia. I work mainly with ChIP-Seq and RNA-Seq data. I'm proficient in R.

Posts by patelk26

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Rename fasta headers using a variable already present in the header?
... Try this: grep '>' LARGE_MSA.fna | sed 's/>.*.gene=/>/' | sed 's/].*//' ...
written 12 days ago by patelk26100
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Answer: A: Affymetrix probesets to Gene symbols
... You can find your answer here: [Annotate Affymetrix probesets to Gene symbols][1] [1]: https://www.biostars.org/p/332461/#332474 ...
written 12 days ago by patelk26100
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Comment: C: How to create matrix for larger data set?
... This can be done in R. library(readxl) library(dplyr) df <- read_excel('data.xlsx') # reading in your data df %>% gather(key = 'genesB', value, -c(genesA)) %>% filter(value > 0) %>% select(genesA, genesB) %>% rename(Protein.B = genesB ...
written 20 days ago by patelk26100
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Answer: A: sed command to extract sequence
... Try this: `sed 's/::g.*(-)//' input.fasta | sed 's/>.*::/>/' > output.fasta` ...
written 21 days ago by patelk26100
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Answer: A: How to identify Transcript Factors (TF) binding to my target sequence
... You can use Homer's `findMotifs.pl ` to find motifs in your sequences. Homer outputs known motifs (motifs matching with the database of motifs) as well as de novo motifs. ...
written 21 days ago by patelk26100
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Comment: C: convert rows to columns in r
... Error indicates you must be having duplicate depmap_ids for same gene. For example: You must be having something like this: ACH-000840 TP53 4.75 ACH-000840 TP53 3.23 So when you try spreading your data frame, it does not know which value to put for gene TP53 depmap_id ACH-000840. Your k ...
written 22 days ago by patelk26100
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Comment: C: snakemake and Star aligner code issue
... May be it should be {wildcards.samples} since you have `SAMPLES= ['A','B','C']` at the beginning of your config file and you are trying to refer to that. ...
written 5 weeks ago by patelk26100
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Comment: C: snakemake and Star aligner code issue
... Have you tried running by changing {sample} to {wildcards.sample} in your shell commands? ...
written 5 weeks ago by patelk26100
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Comment: C: How to handle several measurements of the same gene on one DNA microarray?
... Hi Fabienne, I deal with similar issue, of having multiple expression measurements for a single gene while dealing with microarray data from GEO. I usually deal with it by grouping the gene symbols and calculating the row means, keeping only the row with measurements which has the maximum row mean. ...
written 5 weeks ago by patelk26100
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Comment: C: Microarray Probes to Ensembl ID or Gene ID
... You can try two things (assuming your dataset used Affymetrix Human Genome U133 Plus 2.0 Array): Use `BioMaRt` library(biomaRt) ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") probeids=c('200007_at', '200011_s_at', '200012_x_at') getBM(attributes=c('affy_hg_u133_plus_2 ...
written 5 weeks ago by patelk26100

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