Question

commandlines and sequences

0

Entering edit mode

6.1 years ago

Baby Bioinformatician ▴ 100

Which command can I use to grab the first 10 nucleotides in each line of my nucleotide sequence in a file?

sequence • 1.2k views

ADD COMMENT • link updated 6.1 years ago by GenoMax 148k • written 6.1 years ago by Baby Bioinformatician ▴ 100

2

Entering edit mode

Use google please! enter image description here

ADD REPLY • link 6.1 years ago by ATpoint 86k

0

Entering edit mode

What have you tried? Otherwise this is a pure programming question.

ADD REPLY • link 6.1 years ago by Michael 55k

0

Entering edit mode

I'd suggest starting with the biopython cookbook and tutorial. The solution to your problem is in there.

ADD REPLY • link 6.1 years ago by WouterDeCoster 47k

0

Entering edit mode

Refer to tips and tricks on trimming ngs data online.

ADD REPLY • link 6.1 years ago by cpad0112 21k

score 1 · Answer 1 · 2018-11-23

1

Entering edit mode

6.1 years ago

GenoMax 148k

You can use reformat.sh from BBMap suite to do this.

reformat.sh in=infile.fq out=outfile.fq ftr=9

If you have paired-end data then you would want to use something like this

reformat.sh in1=infile_R1.fq in2=infile_R2.fq out1=outfile_R1.fq out2=outfile_R2.fq  ftr=9

ADD COMMENT • link 6.1 years ago by GenoMax 148k