I have a txt file with data of this form:
@HWI-ST999:188:C49E6ACXX:8:1101:11404:1998/1 NCGAGGGATGGGAGACCTGGTTGGAAATCCGTGGCTGTTTGGTTGGGGGAT + #4=DDFFDHDHHGJIIJIJIFHIIIJJIJJJDHIGIEDGHGI=CGHJJH9> @HWI-ST999:188:C49E6ACXX:8:1101:1754:2212/1 TCGAATGCATGATAACAATAACCCTGGAACAGGCAACCGTTGTCCCTGACC + CCCFFFFFHHHGHJJJJJJJJJJJJJJJJJJJJIJJJJJIIJJJJJJJJJJ
I would like to remove the
/1 of the end of every 5th line.
Is this possible with a one liner in bash, maybe with sed (OSX)?
Context: I extracted reads from a bam file with Bam2Fastq into the format fastq. But the subsequent processing does not cope with the /1 or /2 in my two files of paired-end reads.
Would be more accurate to call this a fastq file, it's not just a txt file...
But someone who does not know what a fastq format is would be put off by it. And basically it can be called a txt file.
That doesn't make sense. You don't want answers from people who don't know what a fastq file is. This is biostars. We read fastq files at breakfast like normal people read the newspaper.
For this question it is unnecessary to know anything about biology. And I want to keep the question as easy to understand as possible. It would be more accurate to call it a fastq file, I guess, but not helpful here and in some cases maybe distracting. Although I guess 99.9% of people here know that it is a fastq file. And for those, I don't need to make it clear anyways.