Removing bases from reads at specific positions (in the middle)

Question

[Rezenman]

Hey guys ! I was looking for a tool to remove a specific number of bases at a specific location (in the middle of the read) from a fastq file, Does anyone know any way of doing it ? Thanks !

[GenoMax]

I am curious about the use case for this request. What are you trying to do? Remove N's? By removing bases in the middile of read you are going to change the context of the remainder of bases.

[Rezenman]

Hey, I am working on a very specific custom pipeline in which I have to remove 4 bases from the middle read - they are found in the same position in all of the reads

[GenoMax]

If the sequences are different but their position is identical then you may need to write custom code to remove those bases.

Answer 1

[Buffo]

You can use Trimmomatic: A flexible read trimming tool for Illumina NGS data

[Rezenman]

Hey Buffo Thanks for the suggestion, however, I have found that all tools -including the abovementioned can only remove bases from the beginning /end of the read I am looking for a tool to help me remove 4 bases in the middle of the read according to their position. I can also settle for a tool that will help me merge sequences found in different Fastq files if you know any? Thanks

[Buffo]

Oh i see,

I am looking for a tool to help me remove 4 bases in the middle of the read according to their position.

For this you cand use biopieces, command find_adaptor.

I can also settle for a tool that will help me merge sequences found in different Fastq files if you know any?

For merge fastq files in a single one, type in a unix shell:

cat file1.fastq file_2.fastq > merged_seqs.fastq