User: martyferr90

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martyferr9020
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Posts by martyferr90

<prev • 9 results • page 1 of 1 • next >
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RAPIDR mask and build the reference
... Hi all! I'm new to RAPIDR usage and i have some problems. First of all I would to know how I can obtain a mask bed file to perform the makeBinnedCountsFile with the mask. The second question is: I'm trying to build a reference and using the code on the exemple (demo file in the package), but I r ...
R ngs bam rapdir nipt written 6 days ago by martyferr9020
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Comment: C: Issue with RAPIDR
... HI, you were right. Now I can create the binned count fille, but I have another question: to perform masking step I need a mask bed file, where I can finds it? Is the output.fname.mask file that the package produce with the first binned? And if it is that file, how can I convert a .mask file in a .b ...
written 6 days ago by martyferr9020
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Issue with RAPIDR
... Hi all! I'm trying to use RAPIDR package, but when I start with the first command with the code: > makeBinnedCountsFile(bam.file.list=c("NIPD01.bam","NIPD02.bam"), + sampleIDs = c("sample1", "sample"), + binned.counts.fname = output.fname, + k=20000) It give to m ...
R bam rapidr nipt written 7 days ago by martyferr9020 • updated 7 days ago by Sean Davis23k
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Detect small deletion
... Hi all! I just need an advice: I have to investigate on small deletions that cause a various diseases, and in particular in prenatal testing. Which software could I use? Is there a software where you can insert a list of genes to investigate for this microdeletions? Thank you for your answer! ...
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Comment: C: XHMM and PLINK/Seq problem
... UPDATE: I managed to run the program, and I understand where was the error. In the filtered step, with those parameters, the output file was empty, so I tied to modify the value, in particular minMeanSampleRD. But ther's one more problem. I'm using a known set of BAM files, in which i know who have ...
written 18 months ago by martyferr9020
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XHMM and PLINK/Seq problem
... Hi! I'm trying to use XHMM for CNV detection but I have a few problems: 1) I'm following this quide [url]http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml[/url] for the use and I installed PLINK/Seq tools but when I try to use: "./sources/scripts/interval_list_to_pseq_reg EXOME.interval_list > ...
plinik/seq xhmm cnv written 18 months ago by martyferr9020
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Comment: C: Problem with human_g1k_v37
... Thank you for your help! I'll try to use this file to make my analysis, I'll let you know! ...
written 18 months ago by martyferr9020
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Problem with human_g1k_v37
... Hi! I'm trying to use human_g1k_v37 reference genome and I've download it in .gz format but when I try to extract it I get an error. Is there a way to extract or to download it in uncrompress format? Or is there a way to uncompress it? Thank's ...
reference genome human_g1k_v37 hg19 written 18 months ago by martyferr9020
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ExomeCNV and GATK
... Hi, I'm trying to use ExomeCNV to detect the CNV on 2 chromosomes (13 and 17 for BRCA1 and BRCA2). I use the manual on https://secure.genome.ucla.edu/index.php/ExomeCNV_User_Guide and for first part (the GATK part) I use the code on the instruction with the only variant on reference genome (I use ...
exome gatk exomecnv cnv written 18 months ago by martyferr9020

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