Question: Viewing and editing FASTQ files
1
gravatar for gprashant17
11 months ago by
gprashant1770
gprashant1770 wrote:

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?

ADD COMMENTlink written 11 months ago by gprashant1770
1

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.

ADD REPLYlink written 11 months ago by genomax83k

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

ADD REPLYlink written 11 months ago by gprashant1770

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

ADD REPLYlink written 11 months ago by genomax83k

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

ADD REPLYlink written 11 months ago by gprashant1770
2
gravatar for ATpoint
11 months ago by
ATpoint34k
Germany
ATpoint34k wrote:

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

ADD COMMENTlink written 11 months ago by ATpoint34k

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.

ADD REPLYlink written 11 months ago by gprashant1770
1

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

ADD REPLYlink written 11 months ago by ATpoint34k
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