User: patelk26
patelk26 • 20
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Posts by patelk26
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... 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
patelk26 • 20
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... 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 ...
written 7 days ago by
patelk26 • 20
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... 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
patelk26 • 20
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... 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
patelk26 • 20
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... 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
patelk26 • 20
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... 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
patelk26 • 20
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... 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
patelk26 • 20
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... 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
patelk26 • 20
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