User: patelk26

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patelk2620
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Posts by patelk26

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Answer: A: How to interpret CERES gene scores for genome wide CRISPR-Cas9 knockout screens?
... https://www.biorxiv.org/content/10.1101/160861v1 The above paper about CERES was helpful in explaining CERES as a computation method to estimate gene dependency levels which accounts for the copy number specific effect (regions with high CN causes sequence-independent DNA damage and G2 cell-cycle a ...
written 6 days ago by patelk2620
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How to interpret CERES gene scores for genome wide CRISPR-Cas9 knockout screens?
... Hello, I am using Achilles dataset (DepMap Public 19Q2) which contains the results of genome-scale CRISPR knockout screen to study the effect of genes in survival and proliferation of certain cancer cell lines. I have a data matrix which contains scores for 17,634 genes across 563 cell lines. I do ...
crispr written 7 days ago by patelk2620
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Comment: C: How to Analyze list of ATAC-seq peaks for specific motifs list?
... You can find instance of specific motifs in Homer by providing a motif file. You can run findMotifsGenome.pl with the "-find motif_file.motif" option. Results will be in the form of a tab-delimited text file with each line containing an instance of the motif in the target peaks. findMotifsGeno ...
written 3 months ago by patelk2620
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Comment: C: Error while annotating with Chipseeker
... Your peakfile should have these five tab-delimited columns - - Column1: Unique Peak ID - Column2: chromosome - Column3: starting position - Column4: ending position - Column5: Strand (+/- or 0/1, where 0="+", 1="-") Please ensure your chromosomes have "chr" before the number. ...
written 3 months ago by patelk2620
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Comment: C: Error while annotating with Chipseeker
... http://homer.ucsd.edu/homer/download.html - You will have to download homer software which includes this annotation script http://homer.ucsd.edu/homer/ngs/annotation.html - here's a link with detailed explanation of how Homer performs annotation of peaks. ...
written 3 months ago by patelk2620
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Comment: C: Error while annotating with Chipseeker
... I have not tried to annotate peaks with Chipseeker; I use Homer's annotatePeaks.pl to annotate peaks. annotatePeaks.pl peakfile hg19 > output.txt ...
written 3 months ago by patelk2620
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Answer: A: Taking information from a .txt and converting it to fasta
... I am sure there are more efficient and concise way of doing this, but this gets you the desired result. #!/usr/bin/Python # file to write the results fasta = open("resultingFasta.fa","a") # list to capture results result = [] with open("dna.txt") as fh: for line i ...
written 3 months ago by patelk2620
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Answer: A: MSTRGs are plaguing my RNA-Seq analysis
... Have you tried option -c? This flag will output a file with all transcripts in the provided reference file that are fully covered by the reads. This flag will require Reference annotation file (-G) to be provided. ...
written 5 months ago by patelk2620

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