remove white space in fastq file

Question

[gkarere]

please help remove white space in fastq file

[Pierre Lindenbaum]

duplicate : Please help with removing spaces from fasta file

[Ram]

Note: FASTQ headers might need those spaces, DO NOT REMOVE them unless you fully know what you're doing and why you're doing it.

[gkarere]

please help remove white space in fastq file in mac 12.6.9

[Ram]

please ask question better on forum, please read http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1002202

[gkarere]

I am running mapper. pl on mirDeep2-0.1.0 and some sequence files are kicked out with these messages line " Second line of FASTQ reads file contains whitespace in sequence". "Please make sure your file is in accordance with the FASTQ format specifications"

[Ram]

Why did you add this as an answer? Please learn how to use the forum properly. Read these posts: https://www.biostars.org/tag/how-to/

[Ram]

FASTQ should NOT have white spaces in the read sequence line. Do not just remove them, go back to the source and figure out why they have white spaces.

[eam-hmc]

Do you mean empty lines between sequences? Or spaces within the sequences?

To remove empty lines between sequences I've used sed before:

sed -i '/^$/d' your_fastq_file.fastq

[GenoMax]

No it is spaces within sequences so this answer does not apply.

I am running mapper. pl on mirDeep2-0.1.0 and some sequence files are kicked out with these messages line " Second line of FASTQ reads file contains whitespace in sequence". "

[Ram]

I've moved your post to a comment as it does not answer the top level question.

[gkarere]

Not been able to remove white spaces. I would appreciate any other suggestion

[GenoMax]

Try the following

awk 'NR%4==2 {gsub(" ", "");} {print;}' input.fastq > output.fastq

Replace the names of the files as appropriate.

---

ChatGPT also suggests this python script

def remove_spaces_from_fastq(input_file, output_file):
    with open(input_file, 'r') as infile, open(output_file, 'w') as outfile:
        for line_number, line in enumerate(infile, start=1):
            # Modify the second line (sequence line) by removing spaces
            if line_number % 4 == 2:
                line = line.replace(" ", "")

            # Write the modified or unmodified line to the output file
            outfile.write(line)

if __name__ == "__main__":
    input_fastq = "input.fastq"  # Replace with your input FASTQ file
    output_fastq = "output.fastq"  # Replace with the desired output file name

    remove_spaces_from_fastq(input_fastq, output_fastq)

Save as remove_spaces.py and run.

python remove_spaces.py

NOTE: Pay attention to point @Ram has made a couple of times. If the data is corrupt you are best off procuring a new copy.

[Ram]

ChatGPT hard-coding inputs - looks like it's gone from being a good programmer to being a beginner. Weird AI evolution?

[Ram]

Did you figure out why those white spaces were introduced? Your data is possibly corrupt and you're working to silence the evidence instead of preserving it.