User: Cindy

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Cindy0
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Posts by Cindy

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Picard tools samtofastq for a folder
... That's my final code and it works. First, use SamToFastq to generate *_R1_fq.gz and *_R2_fq.gz, then use mkdir and mv to move all fastq files to a new folder. find /path/to/folder/ -name "*.bam" | while read F ; do java -jar picard.jar SamToFastq \ INPUT=$F \ ...
written 4 days ago by Cindy0 • updated 3 days ago by genomax27k
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Comment: C: Picard tools samtofastq for a folder
... I have tried. ERROE: Neither file nor parent directory exist. I think for the "FASTQ=" and "SECOND_END_FASTQ=" I can not use /path/to/folder/${b%.*}, because it shows output=/path/to/folder/path/to/folder/. If only use FASTQ=${b%.bam}_R1.fq.gz, it works. ...
written 4 days ago by Cindy0
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Comment: C: Picard tools samtofastq for a folder
... I appreciate your help! ...
written 4 days ago by Cindy0
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Comment: C: Picard tools samtofastq for a folder
... Thanks. It works!!! Can I generate a folder call fastq under the "/path/to/folder/" to output all fastq using the same input filename? ...
written 4 days ago by Cindy0
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Comment: C: Picard tools samtofastq for a folder
... I have tried, same error: ERROR: Option 'INPUT' is required. I don't know why it's always request INPUT ...
written 4 days ago by Cindy0
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Comment: C: Picard tools samtofastq for a folder
... erroe msg is INPUT is required. It's kind wired. I think the I=$b is right.... ...
written 4 days ago by Cindy0
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Comment: C: Picard tools samtofastq for a folder
... When I run echo $b done, It listed all bam files in the folder. ...
written 4 days ago by Cindy0
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Picard tools samtofastq for a folder
... I want to use SamToFastq in Picard tools to convert 100 bam files to fastq (pair-end). I wrote a loop, but it does not work. Anyone can help me to look at the code. I have no idea what's going on. Appreciate ahead. #!/bin/bash bamfolder="/path/to/folder/*" for b in $bamfolder do ...
sequencing written 5 days ago by Cindy0
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Comment: C: How to map the reads from a Bam file to another reference genome????
... Thanks. I have used samtools to remap. ...
written 7 days ago by Cindy0
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How to map the reads from a Bam file to another reference genome????
... Dear all, I have got BAM files of mitochondrial DNA sequencing, which were aligned to mtDNA reference genome. Now I want to look at whether those mapped reads also have some overlap with nuclear genome. What should I do? I have extracted mapped reads from bam files, should I just use bwa to align t ...
sequencing written 13 days ago by Cindy0 • updated 13 days ago by WouterDeCoster17k

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