User: jparker4

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jparker420
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Posts by jparker4

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Pseudo-Counts or Zero-Containing True Counts for Mann-Whitney-U Test?
... Any advice on how to correct for these things? Can I use the inputs or IgG samples to correct for mappability by dividing by the counts for either of these samples? ...
written 21 days ago by jparker420
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Comment: C: Pseudo-Counts or Zero-Containing True Counts for Mann-Whitney-U Test?
... The data is ChIP-seq data performed in duplicate. I'm comparing read counts over specific regions of the genome BETWEEN different sets of genes within conditions rather than between conditions, which is why I haven't used DESeq2/edgeR/limma. I normalised by the number of mapped reads. ...
written 26 days ago by jparker420
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Pseudo-Counts or Zero-Containing True Counts for Mann-Whitney-U Test?
... When running Mann-Whitney-U tests on count data out of feature counts, do you know if is correct to converted to pseudo-counts (however you want to do that, x +1 etc) or leave the zeros in? Previously I removed the zeros altogether when comparing counts over specific region of the genome for differe ...
R chip-seq written 26 days ago by jparker420 • updated 26 days ago by Asaf7.6k
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Co-expression analysis for genes coexpressed with gene X, genes X and Y, etc.
... Hi, I have been asked to perform a co-expression analysis to look for genes that are co-expressed with several genes of interest. The individual has requested that I look for genes co-expressed with each of the genes of interest, then look for genes that are co-expressed with two of the genes of int ...
co-expression microarray written 13 months ago by jparker420 • updated 13 months ago by Martombo2.6k
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Advice for indel calling
... Hi, I am doing some indel calling on some RNA-seq data. I wondered if there was a preferred indel caller, and are there any pre-processing steps necessary in an indel calling pipeline, or does it depend on the caller used. Thanks. ...
indel rna-seq written 20 months ago by jparker420 • updated 18 months ago by Biostar ♦♦ 20
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Comment: C: Reordering Bam files based on chromosome number, when the chromosome format is c
... Apologies, that was misleading. It is part of a variant calling pipeline but the actual error occurs when trying to run SplitNCigarReads. The full command I am running is posted below the comment underneath this one. ...
written 21 months ago by jparker420
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Comment: C: Reordering Bam files based on chromosome number, when the chromosome format is c
... Hi, thanks for the reply. Unfortunately the error is occurring when I run SplitNCigarReads, which requires the -U option ALLOW_N_CIGAR_READS. The tool will not let me pass two -U options in, so I'm a bit stuck. Below is the error causing command: java -Xmx10G -Djava.io.tmpdir=/fastdata/mbp15j ...
written 21 months ago by jparker420 • updated 21 months ago by genomax83k
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Reordering Bam files based on chromosome number, when the chromosome format is chr1..etc
... When trying to call variants I get the error message: ##### ERROR MESSAGE: Lexicographically sorted human genome sequence detected in reads. Please see https://software.broadinstitute.org/gatk/documentation/article?id=1328for more information. Error details: reads contigs = [chr1, chr10, chr11, ...
rna-seq snp written 21 months ago by jparker420 • updated 21 months ago by finswimmer13k
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Stastical test for difference between TPMs for two transcript isoforms of a gene
... Hi, I'm having some trouble knowing how best to test for statistical differences within my data. For each sample I mapped using salmon, I have TPM values for two different transcript isoforms of a particular gene and I want to compare the set of TPM values for one isoform to the set of values for th ...
rna-seq written 3.2 years ago by jparker420
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How to access VCF files for Genotype Tissue Expression (GTEx) data
... Hello, I have access to the raw GTEx data and am trying to the download VCF files containing the SNP data for each of the donors within the dataset. However, I cannot find where these files are kept/how to access them. Any help would be much appreciated. ...
vcf snp gtex written 3.4 years ago by jparker420 • updated 3.3 years ago by Tao370

Latest awards to jparker4

Popular Question 13 months ago, created a question with more than 1,000 views. For How to access VCF files for Genotype Tissue Expression (GTEx) data
Popular Question 21 months ago, created a question with more than 1,000 views. For How to access VCF files for Genotype Tissue Expression (GTEx) data

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