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please help remove white space in fastq file in mac 12.6.9
please ask question better on forum, please read http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1002202
duplicate : Please help with removing spaces from fasta file
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.
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"
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/
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.
Do you mean empty lines between sequences? Or spaces within the sequences?
To remove empty lines between sequences I've used
sedbefore:No it is spaces
withinsequences so this answer does not apply.I've moved your post to a comment as it does not answer the top level question.
Not been able to remove white spaces. I would appreciate any other suggestion
Try the following
Replace the names of the files as appropriate.
ChatGPT also suggests this python script
Save as
remove_spaces.pyand run.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.
ChatGPT hard-coding inputs - looks like it's gone from being a good programmer to being a beginner. Weird AI evolution?
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.