User: mychung

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mychung0
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Taiwan
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2 months ago
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4 years, 2 months ago
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m******@ym.edu.tw

Posts by mychung

<prev • 11 results • page 1 of 2 • next >
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Comment: C: BAM files cannot be downloaded and failed MergeSamFiles Fatal error: Exit code 1
... My jobs appear to be running fine now. However, .bam files still cannot be downloaded. ...
written 5 months ago by mychung0
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BAM files cannot be downloaded and failed MergeSamFiles Fatal error: Exit code 127 ()
... Hi, I've mapped some WES and WGS data through the pipeline. For the past two days, either the "merge" of mapped bam files cannot be performed or the merged, sorted, markduplicates, cleaned datasets cannot be downloaded. The .bam files can be visualized locally and they are fine. Note: 1. .bai can ...
bam written 5 months ago by mychung0 • updated 5 months ago by Jennifer Hillman Jackson25k
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Comment: C: BWA-MEM Fatal error: Matched on ERROR
... Hi Jen, I noticed that the failed MarkDuplicates using sorted BAM may be due to errors in merged BAM regardless of validation stringency (Lenient or Silent). The following is an example of stderr under Lenient stringency. How should SAM validation errors like this be fixed? Please advise. Thank ...
written 5 months ago by mychung0
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Comment: C: BWA-MEM Fatal error: Matched on ERROR
... Hi, Jen Thank you very much for the support and suggestions. It's good to know that the BAM files are intact. As suggested, a BAM file was sorted before performing MarkDuplicatesWithMateCigar. Unfortunately, it failed again. The error message is as the following, [bam_header_read] EOF marker is ...
written 6 months ago by mychung0
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BWA-MEM Fatal error: Matched on ERROR
... Hi, I was aligning with bwa-mem on a 52.7GB trimmed paired fastq from WGS under the following conditions Will you select a reference genome from your history or use a built-in index? cached Using reference genome hg19 Single or Paired-end reads paired_iv Select fastq dataset 1: F30_S11_L001_ ...
alignment software error written 6 months ago by mychung0 • updated 6 months ago by Jennifer Hillman Jackson25k
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Comment: C: Can we map fastq files with paired ends using bwa mem on galaxy?
... Select "paired interleaved" under "single or paired-end reads" will do. ...
written 6 months ago by mychung0
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Comment: C: Can we map fastq files with paired ends using bwa mem on galaxy?
... If read1 and read2 are in seperate fastq, then we specify each in the pair selection. For a fastq file contain both read1 and read2, how should the two reads be specified in the pair selection? Select the same fastq in both? Thank you! ...
written 6 months ago by mychung0
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Can we map fastq files with paired ends using bwa mem on galaxy?
... I have a collection of timmed fastq files from WES, each contain paired ends. Is it possible to map these files using bwa mem on galaxy? ...
alignment written 6 months ago by mychung0 • updated 6 months ago by Devon Ryan1.9k
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Comment: C: uploaded FASTQ not showning in the pulldown menu
... Hi Jennifer and Bjoern, Thank you both for help. It worked after converting by "fastq groomer". ...
written 4.2 years ago by mychung0
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Comment: C: uploaded FASTQ not showning in the pulldown menu
... Hi Jennifer and Bjoern, Thank you both for help. It worked after converting by "fastq groomer". ...
written 4.2 years ago by mychung0

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Popular Question 4.1 years ago, created a question with more than 1,000 views. For uploaded FASTQ not showning in the pulldown menu

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