Tutorial:
Create de novo repeat library
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Juke34
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Recent Replies
Answer: scRNAseq Differential expression analysis
by
MVJ
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0
Thank you so much for all the replies! I am new to the field and all of the insights are really helpful and much appreciated
Answer: Dotplot : how to self-define the range of legend
by
Sashu
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30
add `scale_size_continuous(limits = c(0, 100), breaks = c(0, 25, 50, 75, 100))`
DotPlot(mrc.har_sub, features = markers.to.plot , dot.scal…
Comment: genome data downloads for various strains
by
iftikharmaryam123
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Sorry i am new in that website and dont know too much about it
Answer: How to create structural variants ground truth for alignment of two long-read ge
by
Thomas
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Thank you very much for your response!
What I tried for now is calling the SVs from the assembly alignment and validating the individua…
Comment: Using STAR aligner to build index of hg38
by
Grace
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But I am going to do variant calling later, so I think STAR is more appropriate. Thank you.
Comment: Merging the filename with tsv files for master file
by
smrutimayipanda
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20
this is the code which I have written:
import os
import pandas as pd
# Get the list of all the orf.tsv files
orf_tsv_…
Comment: Weirdness in annotation (missing allele frequencies)
by
Jeremy Leipzig
21k
There are plenty of variants that don't exist in gnomAD - only 759M SNPs (chr-pos-ref-alt) out of a possible 9B. Your question is a bit con…
Comment: Modify the code to take most abundant reads from a cluster and process it.
by
Mohd
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40
Hi, Thanks for the help. I am just a beginner and the code was written by someone else, I am trying to modify it for myself. I will try to …
Comment: Hugo_Symbol to Entrez ID
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GenoMax
134k
Using `EntrezDirect` ([**LINK**][1]):
$ esearch -db gene -query "TSPAN6 [gene] AND human [orgn]" | esummary | xtract -pattern Document…
Comment: Ties in reranked list
by
Hamza
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0
I had actually accidentally used ranks instead of Entrez gene ids (but switched later to human Ensembl gene ids). However, without your com…
Comment: Hugo_Symbol to Entrez ID
by
shakyaram079
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Yes sure. These are all gene IDs BZRAP1, C19orf60, TCEB3 and so on.
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
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Y
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0
I tried the commands you recommended in the bash/command line. When I tried `find "${bam_directory}" -type f -name "*.bam" | xargs samtools…
Comment: Hugo_Symbol to Entrez ID
by
GenoMax
134k
Can you provide some examples of HUGO ID's you are unable to convert?
Comment: Using STAR aligner to build index of hg38
by
GenoMax
134k
GTF file includes gene models/annotation information.
You could also use a program like `salmon/kallisto` with just human transcriptome to…
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