User: errityf

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errityf0
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Posts by errityf

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Filtering using BED file
... I have generated mpileups and I wish to filter the desired variants using a BED file. I have done this in the mpileup tool but it then wont allow me to filter further using VarScan. Is there a tool that will allow me to select variants based on a BED file after I generate the mpileup? Thanks. ...
filtering mpileup vcf bed file written 18 months ago by errityf0 • updated 18 months ago by Devon Ryan1.9k
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Comment: C: Need help with mpileup tool on Galaxy
... Hello Jen, Yes hg19 was used for BAM dataset and for subsequent analysis. I am doing a basic bioinformatics analysis research project for my masters degree. It requires me to align bam files and generate mpileup using samtools. The datasets are from an IonTorrent sequencer- I am wondering if this wo ...
written 19 months ago by errityf0
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Having trouble viewing mpileup
... I have generated an mpileup using one bam file, just wondering what is the best way to view this? When I view in IGV I just get a series of boxes in a diagonal pattern- which doesn't seem right. Where could I be going wrong? I have sorted and indexed the bam file and aligned it using both BWA and Bo ...
mpileup written 19 months ago by errityf0 • updated 19 months ago by Jennifer Hillman Jackson23k
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Need help with mpileup tool on Galaxy
... Hey, I'm new to bioinformatics and I'm having some trouble creating an mpileup. Trying to create an mpileup for a bam file. When I create one using the tool on samtools, using default settings it looks incorrect when I try to view it on IGV. I have viewed the .bam file on IGV before creating the mpi ...
samtools mpileup galaxy written 19 months ago by errityf0 • updated 19 months ago by Jennifer Hillman Jackson23k

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