User: jparker4

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jparker420
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Posts by jparker4

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Comment: C: Is there a reason for less IgG occupancy around the promoters of highly expresse
... The data is presented as a metagene. The panel on the left is bottom 10% as regard expression levels and the right is the top 10%. The counts over the region were divided by the number of mapped reads for that sample and multiplied by 1 million to get counts per million. The samples were then divide ...
written 7 weeks ago by jparker420 • updated 7 weeks ago by ATpoint44k
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Is there a reason for less IgG occupancy around the promoters of highly expressed genes?
... It seems that there a consistent trend in my ChIP data that more highly expressed genes appear to have less IgG occupancy around the promoter. Is this known to happen/is there an established reason for this? I thought it could be due to higher polII occupancy in these genes preventing other protein ...
igg chip-seq written 7 weeks ago by jparker420
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Why are there regions missing from mappability tracks provided by UCSC?
... To get the mappabiity tracks, I downloaded them from the link provided by UCSC (http://hgdownload.soe.ucsc.edu/gbdb/hg38/hoffmanMappability/). The file used for the analysis was k100.Umap.MultiTrackMappability.bw. Once downloaded, this was converted from bigWig to Wig using the bigWigtoWig tool from ...
genome mappability written 5 months ago by jparker420 • updated 4 months ago by Biostar ♦♦ 20
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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 8 months 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 8 months 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 8 months ago by jparker420 • updated 8 months ago by Asaf8.5k
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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 21 months ago by jparker420 • updated 21 months ago by Martombo2.7k
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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 2.3 years ago by jparker420 • updated 2.2 years 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 2.4 years 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 2.4 years ago by jparker420 • updated 2.4 years ago by GenoMax94k

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Popular Question 8 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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Popular Question 2.4 years 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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