User: sgujja

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sgujja20
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New User
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United States
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3 weeks, 4 days ago
Joined:
3 years, 11 months ago
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Posts by sgujja

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Help with OrderedList
... I did look at the other biostar post. All the entries are common in both the lists. However, in my example both the lists have only ~130 genes in common. Which is why I am using the mapping option. The mapping file has all the entries from lista and listb in the same order as in the respective lists ...
written 28 days ago by sgujja20
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Comment: C: Help with OrderedList
... I updated the list names and used the optional argument 'mapping' as an input. Running the function 'compareLists' seems to be working now. I just want to make sure that the mapping input is correct. > compareLists(listb, listc, mapping=lista) Simulating random scores... 0%.. ...
written 28 days ago by sgujja20 • updated 28 days ago by genomax47k
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Comment: C: Help with OrderedList
... Hello Lieven, The manual mentions about an optional parameter "mapping" when the two lists being compared are not the same. > – mapping: Maps identifiers between the two lists. This is a matrix with two columns. All items in ID.List1 must match to exactly one entry of column 1 of the mapping, e ...
written 28 days ago by sgujja20
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Comment: A: Help with OrderedList
... This is what I am trying to do: # mapping file lista <- read.table("list_1_2.txt", header=F,sep="\t") lista <- as.matrix(lista) > head(lista) V1 V2 [1,] "LOC101928626" "LOC101928626" [2,] "NADK" "ARHGEF10L" [3,] "PRDM1 ...
written 28 days ago by sgujja20 • updated 28 days ago by genomax47k
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Help with OrderedList
... Hi, I am trying to use OrderedList to compare two gene list which have about ~10% overlapping genes. However, I get an an error running: > compareLists(list2, list3) Error in compareLists(list2, list3) : 1 element(s) of first list not found in second Could you please help. Th ...
R written 28 days ago by sgujja20 • updated 28 days ago by genomax47k
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Comment: C: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
... Thank you so much for the tutorial. I get this error when I run the step to extract clinical details: GSE2034_clindata=getGSEDataTables("GSE2034")[[2]][1:286,] 909 GSM36894 negative 109 0 ER+ 0 913 GSM36911 negative 80 1 ER+ 0 :3: parser error : xmlSAX2StartDocument ...
written 17 months ago by sgujja20
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Tools for classifying human and mouse reads for WGS data
... Hello, I am looking for suggestions on using tools for classifying human and mouse reads for PDX WGS data. Xenome for RNA-Seq works well.Any input on tools designed for DNA-Seq? Thanks ...
wgs pdx written 18 months ago by sgujja20 • updated 18 months ago by Ron730
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Answer: A: CELLULOID: tumor ploidy, cellularity, subclonal copy number events
... Hello, Could you please advise if this works on zebrafish genome to infer ploidy in tumor/normal samples from ExomeSeq Illumina PE reads. Appreciate all the help. Sharvari ...
written 23 months ago by sgujja20
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Comment: C: VCF to MAF conversion for ABSOLUTE
... Hello Daniel, Thanks for the reply. I did download Zv9 VEP annotation: /home/sg15w/.vep/danio_rerio/76_Zv9/Danio_rerio.Zv9.dna.toplevel.fa and for snpeff as well: java -Xmx2g -jar snpEff.jar download -dataDir $SNPEFF_DATA Zv9 On cloning Cyriacs repo perl vcf2maf.pl --input-vcf /project/umw_mi ...
written 3.0 years ago by sgujja20
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VCF to MAF conversion for ABSOLUTE
... Hello, I am writing to seek your help in using the vcf2maf conversion tool for Zebrafish reference genome. The output MAF file will be used as input for running ABSOLUTE. I've cloned the site: https://github.com/dakl/vcf2maf.git and installed VEP as per the instructions in the manual. However, o ...
absolute vcf2maf written 3.0 years ago by sgujja20 • updated 2.9 years ago by shlee60

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Popular Question 18 months ago, created a question with more than 1,000 views. For VCF to MAF conversion for ABSOLUTE

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