Removing bases from reads at specific positions (in the middle)
1
0
Entering edit mode
4.7 years ago
Rezenman • 0

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 !

sequencing Assembly next-gen • 2.0k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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
ADD REPLY

Login before adding your answer.

Traffic: 2064 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6