User: jonessara770

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jonessara770130
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Posts by jonessara770

<prev • 57 results • page 1 of 6 • next >
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Comment: C: How to take reads from WGS fastq files in order to map it with Exome?
... Actually, because my pipeline is not optimized for WGS and it takes a lot of time to run the WGS so I want just subsample and map it to WES? ...
written 6 weeks ago by jonessara770130
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How to take reads from WGS fastq files in order to map it with Exome?
... Hi I have a fastq files from WGS but I want to subsample the reads and just runs it as WES, is there a way to do that? Thanks Sara ...
wgs written 6 weeks ago by jonessara770130
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Comment: C: CNVkit for germline samples
... Hi Eric, This link https://github.com/etal/cnvkit/blob/master/scripts/cn_ztest.py Does not work. Would it be possible, please, to share your code with me too? Thanks ...
written 7 weeks ago by jonessara770130
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my bam file contains both single-end and paired-end. How can I convert bam to fastq so that fastq contains only paired-end reads?
... Hi I have a bam file that contains both single and paired-reads. How can I convert bam to fastq so that fastq contains only paired-end reads? Thanks ...
wes written 10 weeks ago by jonessara770130 • updated 10 weeks ago by Pierre Lindenbaum114k
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download WGS from dbGAP authorized with prefetch tools
... Hi I would like to download some WGS from dbgap with prefetch.2.9.1. But I get the below message: 2018-08-27T23:17:32 prefetch.2.9.1 warn: Maximum file size download limit is 20GB 2018-08-27T23:17:32 prefetch.2.9.1: 7) 'SRRXXXX' (316GB) is larger than maximum allowed: skipped How can I fix this ...
wgs dbgap written 11 weeks ago by jonessara770130 • updated 11 weeks ago by ATpoint9.3k
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Comment: C: How can I download the fasta file of RepeatMasker UCSC table directly?
... Yes, I did and I save the file but it is truncated from chr18 upwards. ...
written 3 months ago by jonessara770130
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Comment: C: How can I download the fasta file of RepeatMasker UCSC table directly?
... Thanks! I tied this but the file is truncated. ...
written 3 months ago by jonessara770130
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How can I download the fasta file of RepeatMasker UCSC table directly?
... Hi, I am a newbie in Retrotransposable/repeat elements analysis. I used UCSC table in order to get the sequence of RepeatMasker table in fasta format. When I download it through the webpage, the file is truncated at chr16 and does not have all chromosome. How can I download the fastq file of R ...
te repeat retrotransposable/repeat written 3 months ago by jonessara770130
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Comment: C: interpretation of intronic variant detected by WES
... Thank Kevin, The tools in your previous post are for predicting if a variant affects splicing. right? I did this step before and I know it affects splicing but I don't know how to check if it produces truncating protein. ...
written 3 months ago by jonessara770130
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interpretation of intronic variant detected by WES
... Hi I detected a variant in the intron of a gene that is predicted by MutationFinder to affect splicing by activation of an intronic cryptic acceptor site. What is the method to check if this variant produces truncating proteins or not? btw, my data is WES. Thanks Sara ...
wes written 3 months ago by jonessara770130

Latest awards to jonessara770

Popular Question 3 months ago, created a question with more than 1,000 views. For draw gene on chromosome
Popular Question 3 months ago, created a question with more than 1,000 views. For extract sequence around snp
Student 3 months ago, asked a question with at least 3 up-votes. For How to systematically check if a bam file is truncated
Popular Question 6 months ago, created a question with more than 1,000 views. For ExAC PLI score calculation
Scholar 7 months ago, created an answer that has been accepted. For C: grabix installation from github
Popular Question 8 months ago, created a question with more than 1,000 views. For How to systematically check if a bam file is truncated
Popular Question 14 months ago, created a question with more than 1,000 views. For ExAC PLI score calculation
Popular Question 14 months ago, created a question with more than 1,000 views. For How to systematically check if a bam file is truncated

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