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Viewing and editing FASTQ files
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14 months ago

I have a FastQ file which appears to be a truncated one, due to which there is a formatting error, and I'm neither able to upload it in FASTQC software nor use that for aligning it with a reference Genome. The size of the file is around 16 GB. I want to view where the formatting style error occurred (most probably at the end of the file) and edit in such a way that it follows the correct format.

Doing it in a text editor is nearly impossible because the machine crashes if I try to open such a large file. Is there any other tool I can use to edit a small part of the FastQ file?

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You can also try validateFiles from Jim Kent's utils to see where the problem is. Add execute permission chmod u+x validateFiles after you download.

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Yes, I tried this and located where the error has possibly occurred. I still need a way to correct it.

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If you tell us what the error says we can try to help you fix it.

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As far as I know, the BAM file which I have was generated from a different pipeline and when I try to convert to fastq, it results in a truncated file having format errors like:

1) ^B symbol is present in some places instead of breaking into a new line 2) few incomplete records 3) RNA sequence having characters like B, F, @ apart from ATCG

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3 months ago
ATpoint 17k
Germany

Use repair.sh from BBMap and do not even try text editors. That is both impossible and not reproducible.

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I tried this too, it starts running and shows this error finally:

Invalid maximum heap size: -Xmxm Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.

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This is a java-related error. Please search Stack Exchange for exactly this error, there are several suggestions on that.

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