User: jonessara770

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jonessara770170
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Posts by jonessara770

<prev • 58 results • page 1 of 6 • next >
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How to modify chr naming in bam file: chr -> just number
... Hi, I have a bam file that chromosome names are like chr1, chr2 etc. I want to convert it to the form where chromosome naming is just numbered e.g. 1,2,3. I don't know how to change the below code for removing chr instead of adding it? samtools view -h $B | \ sed -e '/^@SQ/s/SN\:/SN\:chr ...
rna-seq written 9 months ago by jonessara770170 • updated 9 months ago by Istvan Albert ♦♦ 81k
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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 11 months ago by jonessara770170
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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 11 months ago by jonessara770170
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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 12 months ago by jonessara770170
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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 12 months ago by jonessara770170 • updated 12 months ago by Pierre Lindenbaum123k
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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 13 months ago by jonessara770170 • updated 12 months ago by ATpoint23k
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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 13 months ago by jonessara770170
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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 13 months ago by jonessara770170
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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 13 months ago by jonessara770170
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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 14 months ago by jonessara770170

Latest awards to jonessara770

Popular Question 13 months ago, created a question with more than 1,000 views. For draw gene on chromosome
Popular Question 13 months ago, created a question with more than 1,000 views. For extract sequence around snp
Student 14 months ago, asked a question with at least 3 up-votes. For How to systematically check if a bam file is truncated
Popular Question 16 months ago, created a question with more than 1,000 views. For ExAC PLI score calculation
Scholar 17 months ago, created an answer that has been accepted. For C: grabix installation from github
Popular Question 19 months ago, created a question with more than 1,000 views. For How to systematically check if a bam file is truncated
Popular Question 2.1 years ago, created a question with more than 1,000 views. For ExAC PLI score calculation
Popular Question 2.1 years 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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